feat: add user-defined metadata field to tasks (#1555) (#1611)

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com> Co-authored-by: Cedric Hurst <cedric@spantree.net> Closes #1555
2026-01-29 22:02:04 +00:00 · 2026-01-26 17:41:33 +01:00
parent 364a160775
commit c798639d1a
19 changed files with 2541 additions and 59 deletions
--- a/.changeset/task-metadata-field.md
+++ b/.changeset/task-metadata-field.md
@@ -0,0 +1,40 @@
+---
+"task-master-ai": minor
+---
+
+Add optional `metadata` field to tasks for storing user-defined custom data
+
+Tasks and subtasks now support an optional `metadata` field that allows storing arbitrary JSON data such as:
+- External IDs (GitHub issues, Jira tickets, Linear issues)
+- Workflow data (sprints, story points, custom statuses)
+- Integration data (sync timestamps, external system references)
+- Custom tracking (UUIDs, version numbers, audit information)
+
+Key features:
+- **AI-Safe**: Metadata is preserved through all AI operations (update-task, expand, etc.) because AI schemas intentionally exclude this field
+- **Flexible Schema**: Store any JSON-serializable data without schema changes
+- **Backward Compatible**: The field is optional; existing tasks work without modification
+- **Subtask Support**: Both tasks and subtasks can have their own metadata
+- **MCP Tool Support**: Use `update_task` and `update_subtask` with the `metadata` parameter to update metadata (requires `TASK_MASTER_ALLOW_METADATA_UPDATES=true` in MCP server environment)
+
+Example usage:
+```json
+{
+  "id": 1,
+  "title": "Implement authentication",
+  "metadata": {
+    "githubIssue": 42,
+    "sprint": "Q1-S3",
+    "storyPoints": 5
+  }
+}
+```
+
+MCP metadata update example:
+```javascript
+// With TASK_MASTER_ALLOW_METADATA_UPDATES=true set in MCP env
+update_task({
+  id: "1",
+  metadata: '{"githubIssue": 42, "sprint": "Q1-S3"}'
+})
+```
--- a/apps/docs/capabilities/task-structure.mdx
+++ b/apps/docs/capabilities/task-structure.mdx
@@ -9,7 +9,7 @@ description: "Tasks in Task Master follow a specific format designed to provide
 Tasks in tasks.json have the following structure:

 | Field          | Description                                     | Example                                                |
-| -------------- | ---------------------------------------------- | ------------------------------------------------------ |
+| -------------- | ----------------------------------------------- | ------------------------------------------------------ |
 | `id`           | Unique identifier for the task.                 | `1`                                                    |
 | `title`        | Brief, descriptive title.                       | `"Initialize Repo"`                                    |
 | `description`  | What the task involves.                         | `"Create a new repository, set up initial structure."` |
@@ -19,6 +19,7 @@ Tasks in tasks.json have the following structure:
 | `details`      | Implementation instructions.                    | `"Use GitHub client ID/secret, handle callback..."`    |
 | `testStrategy` | How to verify success.                          | `"Deploy and confirm 'Hello World' response."`         |
 | `subtasks`     | Nested subtasks related to the main task.       | `[{"id": 1, "title": "Configure OAuth", ...}]`         |
+| `metadata`     | Optional user-defined data (see below).         | `{"githubIssue": 42, "sprint": "Q1-S3"}`               |

 ## Task File Format

@@ -38,6 +39,158 @@ Individual task files follow this format:
 <verification approach>
 ```

+## User-Defined Metadata Field
+
+The `metadata` field allows you to store arbitrary custom data on tasks without requiring schema changes. This is useful for:
+
+- **External IDs**: Link tasks to GitHub issues, Jira tickets, Linear issues, etc.
+- **Workflow data**: Track sprints, story points, custom statuses
+- **Integration data**: Store sync timestamps, external system references
+- **Custom tracking**: UUIDs, version numbers, audit information
+
+### Key Characteristics
+
+<CardGroup cols={2}>
+  <Card title="Fully Optional" icon="toggle-off">
+    The field is optional. Existing tasks work without it.
+  </Card>
+
+<Card title="AI-Safe" icon="shield">
+  AI operations preserve your metadata - it's never overwritten by AI.
+</Card>
+
+<Card title="Flexible Schema" icon="shapes">
+  Store any JSON-serializable data: strings, numbers, objects, arrays.
+</Card>
+
+  <Card title="Subtask Support" icon="list-tree">
+    Both tasks and subtasks can have their own metadata.
+  </Card>
+</CardGroup>
+
+### Usage Examples
+
+**GitHub Issue Linking**
+
+```json
+{
+  "id": 1,
+  "title": "Implement authentication",
+  "metadata": {
+    "githubIssue": 42,
+    "githubIssueUrl": "https://github.com/org/repo/issues/42"
+  }
+}
+```
+
+**Sprint & Project Management**
+
+```json
+{
+  "id": 2,
+  "title": "Refactor API endpoints",
+  "metadata": {
+    "sprint": "Q1-S3",
+    "storyPoints": 5,
+    "epic": "API Modernization"
+  }
+}
+```
+
+**External System Integration**
+
+```json
+{
+  "id": 3,
+  "title": "Fix login bug",
+  "metadata": {
+    "jira": {
+      "key": "PROJ-123",
+      "type": "bug",
+      "priority": "P1"
+    },
+    "importedAt": "2024-01-15T10:30:00Z",
+    "lastSyncedAt": "2024-01-20T14:00:00Z"
+  }
+}
+```
+
+**Stable UUID Tracking**
+
+```json
+{
+  "id": 4,
+  "title": "Add user preferences",
+  "metadata": {
+    "uuid": "550e8400-e29b-41d4-a716-446655440000",
+    "version": 2,
+    "createdBy": "import-script"
+  }
+}
+```
+
+<Warning>
+  **Security Note**: Do not store secrets, API keys, or sensitive credentials in
+  the metadata field. Task data may be visible in logs, exports, or shared with
+  AI providers.
+</Warning>
+
+### Metadata Behavior
+
+| Operation        | Metadata Behavior                                            |
+| ---------------- | ------------------------------------------------------------ |
+| `parse-prd`      | New tasks are created without metadata                       |
+| `update-task`    | Existing metadata is preserved unless explicitly changed     |
+| `expand`         | Parent task metadata is preserved; subtasks don't inherit it |
+| `update-subtask` | Subtask metadata is preserved                                |
+| Manual edit      | You can add/modify metadata directly in tasks.json           |
+| MCP (with flag)  | Use the `metadata` parameter to explicitly update metadata   |
+
+### Updating Metadata via MCP
+
+The `update_task` and `update_subtask` MCP tools support a `metadata` parameter for updating task metadata. This feature is disabled by default for safety.
+
+**To enable MCP metadata updates:**
+
+Add `TASK_MASTER_ALLOW_METADATA_UPDATES=true` to your MCP server environment configuration in `.mcp.json`:
+
+```json
+{
+  "mcpServers": {
+    "task-master-ai": {
+      "command": "npx",
+      "args": ["-y", "task-master-ai"],
+      "env": {
+        "TASK_MASTER_ALLOW_METADATA_UPDATES": "true",
+        "ANTHROPIC_API_KEY": "your_key_here"
+      }
+    }
+  }
+}
+```
+
+**Usage example:**
+
+```javascript
+// Update task metadata (merges with existing)
+update_task({
+  id: "1",
+  projectRoot: "/path/to/project",
+  metadata: '{"githubIssue": 42, "sprint": "Q1-S3"}'
+})
+
+// Update only metadata (no prompt required)
+update_task({
+  id: "1",
+  projectRoot: "/path/to/project",
+  metadata: '{"status": "reviewed"}'
+})
+```
+
+<Note>
+  The `metadata` parameter accepts a JSON string. The new metadata is merged with existing metadata, allowing you to update specific fields without losing others.
+</Note>
+
 ## Features in Detail

 <AccordionGroup>
@@ -56,7 +209,7 @@ The generated report contains:
 - Recommended number of subtasks based on complexity
 - AI-generated expansion prompts customized for each task
 - Ready-to-run expansion commands directly within each task analysis
-</Accordion>
+  </Accordion>

 <Accordion title="Viewing Complexity Report">
 The `complexity-report` command:
@@ -67,7 +220,7 @@ The `complexity-report` command:
 - Highlights tasks recommended for expansion based on threshold score
 - Includes ready-to-use expansion commands for each complex task
 - If no report exists, offers to generate one on the spot
-</Accordion>
+  </Accordion>

 <Accordion title="Smart Task Expansion">
 The `expand` command automatically checks for and uses the complexity report:
@@ -93,6 +246,7 @@ task-master expand --id=8
 # or expand all tasks
 task-master expand --all
 ```
+
 </Accordion>

 <Accordion title="Finding the Next Task">
@@ -108,7 +262,7 @@ The `next` command:
  - Command to mark the task as in-progress
  - Command to mark the task as done
  - Commands for working with subtasks
-</Accordion>
+    </Accordion>

 <Accordion title="Viewing Specific Task Details">
 The `show` command:
@@ -119,7 +273,7 @@ The `show` command:
 - For subtasks, shows parent task relationship
 - Provides contextual action suggestions based on the task's state
 - Works with both regular tasks and subtasks (using the format taskId.subtaskId)
-</Accordion>
+  </Accordion>
 </AccordionGroup>

 ## Best Practices for AI-Driven Development
@@ -130,11 +284,13 @@ The `show` command:
  </Card>

  <Card title="👀 Review Tasks" icon="magnifying-glass">
-    After parsing the PRD, review the tasks to ensure they make sense and have appropriate dependencies.
+    After parsing the PRD, review the tasks to ensure they make sense and have
+    appropriate dependencies.
  </Card>

  <Card title="📊 Analyze Complexity" icon="chart-line">
-    Use the complexity analysis feature to identify which tasks should be broken down further.
+    Use the complexity analysis feature to identify which tasks should be broken
+    down further.
  </Card>

  <Card title="⛓️ Follow Dependencies" icon="link">
@@ -142,7 +298,8 @@ The `show` command:
  </Card>

  <Card title="🔄 Update As You Go" icon="arrows-rotate">
-    If your implementation diverges from the plan, use the update command to keep future tasks aligned.
+    If your implementation diverges from the plan, use the update command to
+    keep future tasks aligned.
  </Card>

  <Card title="📦 Break Down Tasks" icon="boxes-stacked">
@@ -150,14 +307,17 @@ The `show` command:
  </Card>

  <Card title="🔄 Regenerate Files" icon="file-arrow-up">
-    After any updates to tasks.json, regenerate the task files to keep them in sync.
+    After any updates to tasks.json, regenerate the task files to keep them in
+    sync.
  </Card>

  <Card title="💬 Provide Context" icon="comment">
-    When asking the Cursor agent to help with a task, provide context about what you're trying to achieve.
+    When asking the Cursor agent to help with a task, provide context about what
+    you're trying to achieve.
  </Card>

  <Card title="✅ Validate Dependencies" icon="circle-check">
-    Periodically run the validate-dependencies command to check for invalid or circular dependencies.
+    Periodically run the validate-dependencies command to check for invalid or
+    circular dependencies.
  </Card>
 </CardGroup>
--- a/apps/mcp/src/shared/utils.ts
+++ b/apps/mcp/src/shared/utils.ts
@@ -442,3 +442,63 @@ export function withToolContext<TArgs extends { projectRoot?: string }>(
 		}
 	);
 }
+
+/**
+ * Validates and parses metadata string for MCP tools.
+ * Checks environment flag, validates JSON format, and ensures metadata is a plain object.
+ *
+ * @param metadataString - JSON string to parse and validate
+ * @param errorResponseFn - Function to create error response
+ * @returns Object with parsed metadata or error
+ */
+export function validateMcpMetadata(
+	metadataString: string | null | undefined,
+	errorResponseFn: (message: string) => ContentResult
+): { parsedMetadata: Record<string, unknown> | null; error?: ContentResult } {
+	// Return null if no metadata provided
+	if (!metadataString) {
+		return { parsedMetadata: null };
+	}
+
+	// Check if metadata updates are allowed via environment variable
+	const allowMetadataUpdates =
+		process.env.TASK_MASTER_ALLOW_METADATA_UPDATES === 'true';
+	if (!allowMetadataUpdates) {
+		return {
+			parsedMetadata: null,
+			error: errorResponseFn(
+				'Metadata updates are disabled. Set TASK_MASTER_ALLOW_METADATA_UPDATES=true in your MCP server environment to enable metadata modifications.'
+			)
+		};
+	}
+
+	// Parse and validate JSON
+	try {
+		const parsedMetadata = JSON.parse(metadataString);
+
+		// Ensure it's a plain object (not null, not array)
+		if (
+			typeof parsedMetadata !== 'object' ||
+			parsedMetadata === null ||
+			Array.isArray(parsedMetadata)
+		) {
+			return {
+				parsedMetadata: null,
+				error: errorResponseFn(
+					'Invalid metadata: must be a JSON object (not null or array)'
+				)
+			};
+		}
+
+		return { parsedMetadata };
+	} catch (parseError: unknown) {
+		const message =
+			parseError instanceof Error ? parseError.message : 'Unknown parse error';
+		return {
+			parsedMetadata: null,
+			error: errorResponseFn(
+				`Invalid metadata JSON: ${message}. Provide a valid JSON object string.`
+			)
+		};
+	}
+}
--- a/mcp-server/src/core/direct-functions/update-subtask-by-id.js
+++ b/mcp-server/src/core/direct-functions/update-subtask-by-id.js
@@ -17,8 +17,9 @@ import { createLogWrapper } from '../../tools/utils.js';
 * @param {Object} args - Command arguments containing id, prompt, useResearch, tasksJsonPath, and projectRoot.
 * @param {string} args.tasksJsonPath - Explicit path to the tasks.json file.
 * @param {string} args.id - Subtask ID in format "parent.sub".
- * @param {string} args.prompt - Information to append to the subtask.
+ * @param {string} [args.prompt] - Information to append to the subtask. Required unless only updating metadata.
 * @param {boolean} [args.research] - Whether to use research role.
+ * @param {Object} [args.metadata] - Parsed metadata object to merge into subtask metadata.
 * @param {string} [args.projectRoot] - Project root path.
 * @param {string} [args.tag] - Tag for the task (optional)
 * @param {Object} log - Logger object.
@@ -27,8 +28,9 @@ import { createLogWrapper } from '../../tools/utils.js';
 */
 export async function updateSubtaskByIdDirect(args, log, context = {}) {
 	const { session } = context;
-	// Destructure expected args, including projectRoot
-	const { tasksJsonPath, id, prompt, research, projectRoot, tag } = args;
+	// Destructure expected args, including projectRoot and metadata
+	const { tasksJsonPath, id, prompt, research, metadata, projectRoot, tag } =
+		args;

 	const logWrapper = createLogWrapper(log);

@@ -60,9 +62,10 @@ export async function updateSubtaskByIdDirect(args, log, context = {}) {
 			};
 		}

-		if (!prompt) {
+		// At least prompt or metadata is required (validated in MCP tool layer)
+		if (!prompt && !metadata) {
 			const errorMessage =
-				'No prompt specified. Please provide the information to append.';
+				'No prompt or metadata specified. Please provide information to append or metadata to update.';
 			logWrapper.error(errorMessage);
 			return {
 				success: false,
@@ -77,7 +80,7 @@ export async function updateSubtaskByIdDirect(args, log, context = {}) {
 		const useResearch = research === true;

 		log.info(
-			`Updating subtask with ID ${subtaskIdStr} with prompt "${prompt}" and research: ${useResearch}`
+			`Updating subtask with ID ${subtaskIdStr} with prompt "${prompt || '(metadata-only)'}" and research: ${useResearch}`
 		);

 		const wasSilent = isSilentMode();
@@ -98,7 +101,8 @@ export async function updateSubtaskByIdDirect(args, log, context = {}) {
 					projectRoot,
 					tag,
 					commandName: 'update-subtask',
-					outputType: 'mcp'
+					outputType: 'mcp',
+					metadata
 				},
 				'json'
 			);
--- a/mcp-server/src/core/direct-functions/update-task-by-id.js
+++ b/mcp-server/src/core/direct-functions/update-task-by-id.js
@@ -18,9 +18,10 @@ import { findTasksPath } from '../utils/path-utils.js';
 * @param {Object} args - Command arguments containing id, prompt, useResearch, tasksJsonPath, and projectRoot.
 * @param {string} args.tasksJsonPath - Explicit path to the tasks.json file.
 * @param {string} args.id - Task ID (or subtask ID like "1.2").
- * @param {string} args.prompt - New information/context prompt.
+ * @param {string} [args.prompt] - New information/context prompt. Required unless only updating metadata.
 * @param {boolean} [args.research] - Whether to use research role.
 * @param {boolean} [args.append] - Whether to append timestamped information instead of full update.
+ * @param {Object} [args.metadata] - Parsed metadata object to merge into task metadata.
 * @param {string} [args.projectRoot] - Project root path.
 * @param {string} [args.tag] - Tag for the task (optional)
 * @param {Object} log - Logger object.
@@ -29,9 +30,17 @@ import { findTasksPath } from '../utils/path-utils.js';
 */
 export async function updateTaskByIdDirect(args, log, context = {}) {
 	const { session } = context;
-	// Destructure expected args, including projectRoot
-	const { tasksJsonPath, id, prompt, research, append, projectRoot, tag } =
-		args;
+	// Destructure expected args, including projectRoot and metadata
+	const {
+		tasksJsonPath,
+		id,
+		prompt,
+		research,
+		append,
+		metadata,
+		projectRoot,
+		tag
+	} = args;

 	const logWrapper = createLogWrapper(log);

@@ -51,9 +60,10 @@ export async function updateTaskByIdDirect(args, log, context = {}) {
 			};
 		}

-		if (!prompt) {
+		// At least prompt or metadata is required (validated in MCP tool layer)
+		if (!prompt && !metadata) {
 			const errorMessage =
-				'No prompt specified. Please provide a prompt with new information for the task update.';
+				'No prompt or metadata specified. Please provide a prompt with new information or metadata for the task update.';
 			logWrapper.error(errorMessage);
 			return {
 				success: false,
@@ -95,7 +105,7 @@ export async function updateTaskByIdDirect(args, log, context = {}) {
 		const useResearch = research === true;

 		logWrapper.info(
-			`Updating task with ID ${taskId} with prompt "${prompt}" and research: ${useResearch}`
+			`Updating task with ID ${taskId} with prompt "${prompt || '(metadata-only)'}" and research: ${useResearch}`
 		);

 		const wasSilent = isSilentMode();
@@ -116,7 +126,8 @@ export async function updateTaskByIdDirect(args, log, context = {}) {
 					projectRoot,
 					tag,
 					commandName: 'update-task',
-					outputType: 'mcp'
+					outputType: 'mcp',
+					metadata
 				},
 				'json',
 				append || false
--- a/mcp-server/src/tools/update-subtask.js
+++ b/mcp-server/src/tools/update-subtask.js
@@ -7,7 +7,8 @@ import { TaskIdSchemaForMcp } from '@tm/core';
 import {
 	createErrorResponse,
 	handleApiResult,
-	withNormalizedProjectRoot
+	withNormalizedProjectRoot,
+	validateMcpMetadata
 } from '@tm/mcp';
 import { z } from 'zod';
 import { resolveTag } from '../../../scripts/modules/utils.js';
@@ -27,11 +28,22 @@ export function registerUpdateSubtaskTool(server) {
 			id: TaskIdSchemaForMcp.describe(
 				'ID of the subtask to update in format "parentId.subtaskId" (e.g., "5.2"). Parent ID is the ID of the task that contains the subtask.'
 			),
-			prompt: z.string().describe('Information to add to the subtask'),
+			prompt: z
+				.string()
+				.optional()
+				.describe(
+					'Information to add to the subtask. Required unless only updating metadata.'
+				),
 			research: z
 				.boolean()
 				.optional()
 				.describe('Use Perplexity AI for research-backed updates'),
+			metadata: z
+				.string()
+				.optional()
+				.describe(
+					'JSON string of metadata to merge into subtask metadata. Example: \'{"ticketId": "JIRA-456", "reviewed": true}\'. Requires TASK_MASTER_ALLOW_METADATA_UPDATES=true in MCP environment.'
+				),
 			file: z.string().optional().describe('Absolute path to the tasks file'),
 			projectRoot: z
 				.string()
@@ -65,12 +77,29 @@ export function registerUpdateSubtaskTool(server) {
 					);
 				}

+				// Validate metadata if provided
+				const validationResult = validateMcpMetadata(
+					args.metadata,
+					createErrorResponse
+				);
+				if (validationResult.error) {
+					return validationResult.error;
+				}
+				const parsedMetadata = validationResult.parsedMetadata;
+				// Validate that at least prompt or metadata is provided
+				if (!args.prompt && !parsedMetadata) {
+					return createErrorResponse(
+						'Either prompt or metadata must be provided for update-subtask'
+					);
+				}
+
 				const result = await updateSubtaskByIdDirect(
 					{
 						tasksJsonPath: tasksJsonPath,
 						id: args.id,
 						prompt: args.prompt,
 						research: args.research,
+						metadata: parsedMetadata,
 						projectRoot: args.projectRoot,
 						tag: resolvedTag
 					},
--- a/mcp-server/src/tools/update-task.js
+++ b/mcp-server/src/tools/update-task.js
@@ -6,7 +6,8 @@
 import {
 	createErrorResponse,
 	handleApiResult,
-	withNormalizedProjectRoot
+	withNormalizedProjectRoot,
+	validateMcpMetadata
 } from '@tm/mcp';
 import { z } from 'zod';
 import { resolveTag } from '../../../scripts/modules/utils.js';
@@ -30,7 +31,10 @@ export function registerUpdateTaskTool(server) {
 				),
 			prompt: z
 				.string()
-				.describe('New information or context to incorporate into the task'),
+				.optional()
+				.describe(
+					'New information or context to incorporate into the task. Required unless only updating metadata.'
+				),
 			research: z
 				.boolean()
 				.optional()
@@ -41,6 +45,12 @@ export function registerUpdateTaskTool(server) {
 				.describe(
 					'Append timestamped information to task details instead of full update'
 				),
+			metadata: z
+				.string()
+				.optional()
+				.describe(
+					'JSON string of metadata to merge into task metadata. Example: \'{"githubIssue": 42, "sprint": "Q1-S3"}\'. Requires TASK_MASTER_ALLOW_METADATA_UPDATES=true in MCP environment.'
+				),
 			file: z.string().optional().describe('Absolute path to the tasks file'),
 			projectRoot: z
 				.string()
@@ -76,7 +86,23 @@ export function registerUpdateTaskTool(server) {
 					);
 				}

-				// 3. Call Direct Function - Include projectRoot
+				// Validate metadata if provided
+				const validationResult = validateMcpMetadata(
+					args.metadata,
+					createErrorResponse
+				);
+				if (validationResult.error) {
+					return validationResult.error;
+				}
+				const parsedMetadata = validationResult.parsedMetadata;
+				// Validate that at least prompt or metadata is provided
+				if (!args.prompt && !parsedMetadata) {
+					return createErrorResponse(
+						'Either prompt or metadata must be provided for update-task'
+					);
+				}
+
+				// Call Direct Function - Include projectRoot and metadata
 				const result = await updateTaskByIdDirect(
 					{
 						tasksJsonPath: tasksJsonPath,
@@ -84,6 +110,7 @@ export function registerUpdateTaskTool(server) {
 						prompt: args.prompt,
 						research: args.research,
 						append: args.append,
+						metadata: parsedMetadata,
 						projectRoot: args.projectRoot,
 						tag: resolvedTag
 					},
--- a/packages/tm-bridge/src/update-bridge.ts
+++ b/packages/tm-bridge/src/update-bridge.ts
@@ -12,6 +12,10 @@ export interface UpdateBridgeParams extends BaseBridgeParams {
 	prompt: string;
 	/** Whether to append or full update (default: false) */
 	appendMode?: boolean;
+	/** Whether to use research mode (default: false) */
+	useResearch?: boolean;
+	/** Metadata to merge into task (for metadata-only updates or alongside prompt) */
+	metadata?: Record<string, unknown>;
 }

 /**
@@ -45,6 +49,8 @@ export async function tryUpdateViaRemote(
 		projectRoot,
 		tag,
 		appendMode = false,
+		useResearch = false,
+		metadata,
 		isMCP = false,
 		outputFormat = 'text',
 		report
@@ -76,7 +82,9 @@ export async function tryUpdateViaRemote(
 	try {
 		// Call the API storage method which handles the remote update
 		await tmCore.tasks.updateWithPrompt(String(taskId), prompt, tag, {
-			mode
+			mode,
+			useResearch,
+			...(metadata && { metadata })
 		});

 		if (spinner) {
--- a/packages/tm-core/src/common/types/index.ts
+++ b/packages/tm-core/src/common/types/index.ts
@@ -156,6 +156,13 @@ export interface Task extends TaskImplementationMetadata {
 	recommendedSubtasks?: number;
 	expansionPrompt?: string;
 	complexityReasoning?: string;
+
+	/**
+	 * User-defined metadata that survives all task operations.
+	 * Use for external IDs, custom workflow data, integrations, etc.
+	 * This field is preserved through AI operations, updates, and serialization.
+	 */
+	metadata?: Record<string, unknown>;
 }

 /**
--- a/packages/tm-core/src/modules/storage/adapters/file-storage/file-storage.ts
+++ b/packages/tm-core/src/modules/storage/adapters/file-storage/file-storage.ts
@@ -283,6 +283,7 @@ export class FileStorage implements IStorage {

 	/**
 	 * Normalize task IDs - keep Task IDs as strings, Subtask IDs as numbers
+	 * Note: Uses spread operator to preserve all task properties including user-defined metadata
 	 */
 	private normalizeTaskIds(tasks: Task[]): Task[] {
 		return tasks.map((task) => ({
@@ -372,9 +373,37 @@ export class FileStorage implements IStorage {
 			throw new Error(`Task ${taskId} not found`);
 		}

+		const existingTask = tasks[taskIndex];
+
+		// Preserve subtask metadata when subtasks are updated
+		// AI operations don't include metadata in returned subtasks
+		let mergedSubtasks = updates.subtasks;
+		if (updates.subtasks && existingTask.subtasks) {
+			mergedSubtasks = updates.subtasks.map((updatedSubtask) => {
+				// Type-coerce IDs for comparison; fall back to title match if IDs don't match
+				const originalSubtask = existingTask.subtasks?.find(
+					(st) =>
+						String(st.id) === String(updatedSubtask.id) ||
+						(updatedSubtask.title && st.title === updatedSubtask.title)
+				);
+				// Merge metadata: preserve original and add/override with new
+				if (originalSubtask?.metadata || updatedSubtask.metadata) {
+					return {
+						...updatedSubtask,
+						metadata: {
+							...(originalSubtask?.metadata || {}),
+							...(updatedSubtask.metadata || {})
+						}
+					};
+				}
+				return updatedSubtask;
+			});
+		}
+
 		tasks[taskIndex] = {
-			...tasks[taskIndex],
+			...existingTask,
 			...updates,
+			...(mergedSubtasks && { subtasks: mergedSubtasks }),
 			id: String(taskId) // Keep consistent with normalizeTaskIds
 		};
 		await this.saveTasks(tasks, tag);
--- a/packages/tm-core/src/modules/tasks/entities/task.entity.spec.ts
+++ b/packages/tm-core/src/modules/tasks/entities/task.entity.spec.ts
@@ -0,0 +1,345 @@
+/**
+ * @fileoverview Unit tests for TaskEntity metadata handling
+ *
+ * Tests the preservation of user-defined metadata through all TaskEntity operations
+ * including construction, serialization, and deserialization.
+ */
+
+import { describe, expect, it } from 'vitest';
+import { TaskEntity } from './task.entity.js';
+import type { Task } from '../../../common/types/index.js';
+
+/**
+ * Creates a minimal valid task for testing
+ */
+function createMinimalTask(overrides: Partial<Task> = {}): Task {
+	return {
+		id: '1',
+		title: 'Test Task',
+		description: 'Test description',
+		status: 'pending',
+		priority: 'medium',
+		dependencies: [],
+		details: 'Task details',
+		testStrategy: 'Test strategy',
+		subtasks: [],
+		...overrides
+	};
+}
+
+describe('TaskEntity', () => {
+	describe('metadata property', () => {
+		it('should preserve metadata through constructor', () => {
+			const metadata = { uuid: '123', custom: 'value' };
+			const task = createMinimalTask({ metadata });
+
+			const entity = new TaskEntity(task);
+
+			expect(entity.metadata).toEqual(metadata);
+		});
+
+		it('should handle undefined metadata', () => {
+			const task = createMinimalTask();
+			// Explicitly not setting metadata
+
+			const entity = new TaskEntity(task);
+
+			expect(entity.metadata).toBeUndefined();
+		});
+
+		it('should handle empty metadata object', () => {
+			const task = createMinimalTask({ metadata: {} });
+
+			const entity = new TaskEntity(task);
+
+			expect(entity.metadata).toEqual({});
+		});
+
+		it('should preserve metadata with string values', () => {
+			const metadata = { externalId: 'EXT-123', source: 'jira' };
+			const task = createMinimalTask({ metadata });
+
+			const entity = new TaskEntity(task);
+
+			expect(entity.metadata).toEqual(metadata);
+		});
+
+		it('should preserve metadata with number values', () => {
+			const metadata = { priority: 5, score: 100 };
+			const task = createMinimalTask({ metadata });
+
+			const entity = new TaskEntity(task);
+
+			expect(entity.metadata).toEqual(metadata);
+		});
+
+		it('should preserve metadata with boolean values', () => {
+			const metadata = { isBlocking: true, reviewed: false };
+			const task = createMinimalTask({ metadata });
+
+			const entity = new TaskEntity(task);
+
+			expect(entity.metadata).toEqual(metadata);
+		});
+
+		it('should preserve metadata with nested objects', () => {
+			const metadata = {
+				jira: {
+					key: 'PROJ-123',
+					sprint: {
+						id: 5,
+						name: 'Sprint 5'
+					}
+				}
+			};
+			const task = createMinimalTask({ metadata });
+
+			const entity = new TaskEntity(task);
+
+			expect(entity.metadata).toEqual(metadata);
+		});
+
+		it('should preserve metadata with arrays', () => {
+			const metadata = {
+				labels: ['bug', 'high-priority'],
+				relatedIds: [1, 2, 3]
+			};
+			const task = createMinimalTask({ metadata });
+
+			const entity = new TaskEntity(task);
+
+			expect(entity.metadata).toEqual(metadata);
+		});
+
+		it('should preserve metadata with null values', () => {
+			const metadata = { deletedAt: null, archivedBy: null };
+			const task = createMinimalTask({ metadata });
+
+			const entity = new TaskEntity(task);
+
+			expect(entity.metadata).toEqual(metadata);
+		});
+
+		it('should preserve complex mixed metadata', () => {
+			const metadata = {
+				externalId: 'EXT-456',
+				score: 85,
+				isUrgent: true,
+				tags: ['frontend', 'refactor'],
+				integration: {
+					source: 'github',
+					issueNumber: 123,
+					labels: ['enhancement']
+				},
+				timestamps: {
+					importedAt: '2024-01-15T10:00:00Z',
+					lastSynced: null
+				}
+			};
+			const task = createMinimalTask({ metadata });
+
+			const entity = new TaskEntity(task);
+
+			expect(entity.metadata).toEqual(metadata);
+		});
+	});
+
+	describe('toJSON() with metadata', () => {
+		it('should include metadata in toJSON output', () => {
+			const metadata = { uuid: '123', custom: 'value' };
+			const task = createMinimalTask({ metadata });
+			const entity = new TaskEntity(task);
+
+			const json = entity.toJSON();
+
+			expect(json.metadata).toEqual(metadata);
+		});
+
+		it('should include undefined metadata in toJSON output', () => {
+			const task = createMinimalTask();
+			const entity = new TaskEntity(task);
+
+			const json = entity.toJSON();
+
+			expect(json.metadata).toBeUndefined();
+		});
+
+		it('should include empty metadata object in toJSON output', () => {
+			const task = createMinimalTask({ metadata: {} });
+			const entity = new TaskEntity(task);
+
+			const json = entity.toJSON();
+
+			expect(json.metadata).toEqual({});
+		});
+
+		it('should preserve nested metadata through toJSON', () => {
+			const metadata = {
+				integration: {
+					source: 'linear',
+					config: {
+						apiKey: 'redacted',
+						projectId: 'proj_123'
+					}
+				}
+			};
+			const task = createMinimalTask({ metadata });
+			const entity = new TaskEntity(task);
+
+			const json = entity.toJSON();
+
+			expect(json.metadata).toEqual(metadata);
+		});
+	});
+
+	describe('round-trip preservation', () => {
+		it('should preserve metadata through full round-trip', () => {
+			const originalMetadata = {
+				uuid: '550e8400-e29b-41d4-a716-446655440000',
+				externalSystem: 'jira',
+				customField: { nested: 'value' }
+			};
+			const originalTask = createMinimalTask({ metadata: originalMetadata });
+
+			// Task -> TaskEntity -> toJSON() -> TaskEntity -> toJSON()
+			const entity1 = new TaskEntity(originalTask);
+			const json1 = entity1.toJSON();
+			const entity2 = new TaskEntity(json1);
+			const json2 = entity2.toJSON();
+
+			expect(json2.metadata).toEqual(originalMetadata);
+		});
+
+		it('should preserve all task fields alongside metadata', () => {
+			const metadata = { custom: 'data' };
+			const task = createMinimalTask({
+				id: '42',
+				title: 'Important Task',
+				description: 'Do the thing',
+				status: 'in-progress',
+				priority: 'high',
+				dependencies: ['1', '2'],
+				details: 'Detailed info',
+				testStrategy: 'Unit tests',
+				tags: ['urgent'],
+				metadata
+			});
+
+			const entity = new TaskEntity(task);
+			const json = entity.toJSON();
+
+			expect(json.id).toBe('42');
+			expect(json.title).toBe('Important Task');
+			expect(json.description).toBe('Do the thing');
+			expect(json.status).toBe('in-progress');
+			expect(json.priority).toBe('high');
+			expect(json.dependencies).toEqual(['1', '2']);
+			expect(json.details).toBe('Detailed info');
+			expect(json.testStrategy).toBe('Unit tests');
+			expect(json.tags).toEqual(['urgent']);
+			expect(json.metadata).toEqual(metadata);
+		});
+	});
+
+	describe('fromObject() with metadata', () => {
+		it('should preserve metadata through fromObject', () => {
+			const metadata = { externalId: 'EXT-789' };
+			const task = createMinimalTask({ metadata });
+
+			const entity = TaskEntity.fromObject(task);
+
+			expect(entity.metadata).toEqual(metadata);
+		});
+
+		it('should handle undefined metadata in fromObject', () => {
+			const task = createMinimalTask();
+
+			const entity = TaskEntity.fromObject(task);
+
+			expect(entity.metadata).toBeUndefined();
+		});
+	});
+
+	describe('fromArray() with metadata', () => {
+		it('should preserve metadata on all tasks through fromArray', () => {
+			const task1 = createMinimalTask({
+				id: '1',
+				metadata: { source: 'import1' }
+			});
+			const task2 = createMinimalTask({
+				id: '2',
+				metadata: { source: 'import2' }
+			});
+			const task3 = createMinimalTask({ id: '3' }); // No metadata
+
+			const entities = TaskEntity.fromArray([task1, task2, task3]);
+
+			expect(entities).toHaveLength(3);
+			expect(entities[0].metadata).toEqual({ source: 'import1' });
+			expect(entities[1].metadata).toEqual({ source: 'import2' });
+			expect(entities[2].metadata).toBeUndefined();
+		});
+
+		it('should preserve different metadata structures across tasks', () => {
+			const tasks = [
+				createMinimalTask({ id: '1', metadata: { simple: 'value' } }),
+				createMinimalTask({
+					id: '2',
+					metadata: { nested: { deep: { value: 123 } } }
+				}),
+				createMinimalTask({ id: '3', metadata: { array: [1, 2, 3] } }),
+				createMinimalTask({ id: '4', metadata: {} })
+			];
+
+			const entities = TaskEntity.fromArray(tasks);
+			const jsons = entities.map((e) => e.toJSON());
+
+			expect(jsons[0].metadata).toEqual({ simple: 'value' });
+			expect(jsons[1].metadata).toEqual({ nested: { deep: { value: 123 } } });
+			expect(jsons[2].metadata).toEqual({ array: [1, 2, 3] });
+			expect(jsons[3].metadata).toEqual({});
+		});
+	});
+
+	describe('no corruption of other fields', () => {
+		it('should not affect other task fields when metadata is present', () => {
+			const taskWithMetadata = createMinimalTask({
+				id: '99',
+				title: 'Original Title',
+				metadata: { someKey: 'someValue' }
+			});
+
+			const entity = new TaskEntity(taskWithMetadata);
+
+			expect(entity.id).toBe('99');
+			expect(entity.title).toBe('Original Title');
+			expect(entity.status).toBe('pending');
+			expect(entity.priority).toBe('medium');
+		});
+
+		it('should not affect subtasks when metadata is present', () => {
+			const taskWithSubtasks = createMinimalTask({
+				metadata: { tracked: true },
+				subtasks: [
+					{
+						id: 1,
+						parentId: '1',
+						title: 'Subtask 1',
+						description: 'Subtask desc',
+						status: 'pending',
+						priority: 'low',
+						dependencies: [],
+						details: '',
+						testStrategy: ''
+					}
+				]
+			});
+
+			const entity = new TaskEntity(taskWithSubtasks);
+
+			expect(entity.subtasks).toHaveLength(1);
+			expect(entity.subtasks[0].title).toBe('Subtask 1');
+			expect(entity.metadata).toEqual({ tracked: true });
+		});
+	});
+});
--- a/packages/tm-core/src/modules/tasks/entities/task.entity.ts
+++ b/packages/tm-core/src/modules/tasks/entities/task.entity.ts
@@ -36,6 +36,7 @@ export class TaskEntity implements Task {
 	recommendedSubtasks?: number;
 	expansionPrompt?: string;
 	complexityReasoning?: string;
+	metadata?: Record<string, unknown>;

 	constructor(data: Task | (Omit<Task, 'id'> & { id: number | string })) {
 		this.validate(data);
@@ -68,6 +69,7 @@ export class TaskEntity implements Task {
 		this.recommendedSubtasks = data.recommendedSubtasks;
 		this.expansionPrompt = data.expansionPrompt;
 		this.complexityReasoning = data.complexityReasoning;
+		this.metadata = data.metadata;
 	}

 	/**
@@ -255,7 +257,8 @@ export class TaskEntity implements Task {
 			complexity: this.complexity,
 			recommendedSubtasks: this.recommendedSubtasks,
 			expansionPrompt: this.expansionPrompt,
-			complexityReasoning: this.complexityReasoning
+			complexityReasoning: this.complexityReasoning,
+			metadata: this.metadata
 		};
 	}

--- a/packages/tm-core/tests/integration/ai-operations/metadata-preservation.test.ts
+++ b/packages/tm-core/tests/integration/ai-operations/metadata-preservation.test.ts
@@ -0,0 +1,481 @@
+/**
+ * @fileoverview Integration tests for metadata preservation across AI operations
+ *
+ * Tests that user-defined metadata survives all AI operations including:
+ * - update-task: AI updates task fields but doesn't include metadata in response
+ * - expand-task: AI generates subtasks but parent task metadata is preserved
+ * - parse-prd: AI generates new tasks without metadata field
+ *
+ * Key insight: AI schemas (base-schemas.js) intentionally EXCLUDE the metadata field.
+ * This means AI responses never include metadata, and the spread operator in
+ * storage/service layers preserves existing metadata during updates.
+ *
+ * These tests simulate what happens when AI operations update tasks - the AI
+ * returns a task object without a metadata field, and we verify that the
+ * existing metadata is preserved through the storage layer.
+ */
+
+import { afterEach, beforeEach, describe, expect, it } from 'vitest';
+import * as fs from 'fs';
+import * as path from 'path';
+import * as os from 'os';
+import { FileStorage } from '../../../src/modules/storage/adapters/file-storage/file-storage.js';
+import type { Task, Subtask } from '../../../src/common/types/index.js';
+
+/**
+ * Creates a minimal valid task for testing
+ */
+function createTask(id: string, overrides: Partial<Task> = {}): Task {
+	return {
+		id,
+		title: `Task ${id}`,
+		description: `Description for task ${id}`,
+		status: 'pending',
+		priority: 'medium',
+		dependencies: [],
+		details: '',
+		testStrategy: '',
+		subtasks: [],
+		...overrides
+	};
+}
+
+/**
+ * Creates a realistic metadata object like external integrations would produce
+ */
+function createRealisticMetadata(): Record<string, unknown> {
+	return {
+		uuid: '550e8400-e29b-41d4-a716-446655440000',
+		githubIssue: 42,
+		sprint: 'Q1-S3',
+		jira: {
+			key: 'PROJ-123',
+			type: 'story',
+			epic: 'EPIC-45'
+		},
+		importedAt: '2024-01-15T10:30:00Z',
+		source: 'github-sync',
+		labels: ['frontend', 'refactor', 'high-priority']
+	};
+}
+
+describe('AI Operation Metadata Preservation - Integration Tests', () => {
+	let tempDir: string;
+	let storage: FileStorage;
+
+	beforeEach(() => {
+		// Create a temp directory for each test
+		tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'taskmaster-ai-test-'));
+		// Create .taskmaster/tasks directory structure
+		const taskmasterDir = path.join(tempDir, '.taskmaster', 'tasks');
+		fs.mkdirSync(taskmasterDir, { recursive: true });
+		storage = new FileStorage(tempDir);
+	});
+
+	afterEach(() => {
+		// Clean up temp directory
+		fs.rmSync(tempDir, { recursive: true, force: true });
+	});
+
+	describe('update-task operation simulation', () => {
+		it('should preserve metadata when AI returns task without metadata field', async () => {
+			// Setup: Task with user metadata
+			const originalMetadata = createRealisticMetadata();
+			const tasks: Task[] = [
+				createTask('1', {
+					title: 'Original Title',
+					description: 'Original description',
+					metadata: originalMetadata
+				})
+			];
+			await storage.saveTasks(tasks);
+
+			// Simulate AI response: AI updates title/description but doesn't include metadata
+			// This is the exact pattern from update-task-by-id.js
+			const aiGeneratedUpdate: Partial<Task> = {
+				title: 'AI Updated Title',
+				description: 'AI refined description with more detail',
+				details: 'AI generated implementation details',
+				testStrategy: 'AI suggested test approach'
+				// Note: NO metadata field - AI schemas don't include it
+			};
+
+			// Apply update through FileStorage (simulating what AI operations do)
+			await storage.updateTask('1', aiGeneratedUpdate);
+
+			// Verify: AI fields updated, metadata preserved
+			const loadedTasks = await storage.loadTasks();
+			expect(loadedTasks[0].title).toBe('AI Updated Title');
+			expect(loadedTasks[0].description).toBe(
+				'AI refined description with more detail'
+			);
+			expect(loadedTasks[0].details).toBe(
+				'AI generated implementation details'
+			);
+			expect(loadedTasks[0].testStrategy).toBe('AI suggested test approach');
+			// Critical: metadata must be preserved
+			expect(loadedTasks[0].metadata).toEqual(originalMetadata);
+		});
+
+		it('should preserve metadata through multiple sequential AI updates', async () => {
+			const metadata = { externalId: 'EXT-999', version: 1 };
+			const tasks: Task[] = [createTask('1', { metadata })];
+			await storage.saveTasks(tasks);
+
+			// First AI update
+			await storage.updateTask('1', { title: 'First AI Update' });
+
+			// Second AI update
+			await storage.updateTask('1', {
+				description: 'Second AI Update adds details'
+			});
+
+			// Third AI update
+			await storage.updateTask('1', { priority: 'high' });
+
+			// Verify metadata survived all updates
+			const loadedTasks = await storage.loadTasks();
+			expect(loadedTasks[0].title).toBe('First AI Update');
+			expect(loadedTasks[0].description).toBe('Second AI Update adds details');
+			expect(loadedTasks[0].priority).toBe('high');
+			expect(loadedTasks[0].metadata).toEqual(metadata);
+		});
+
+		it('should preserve realistic integration metadata during AI operations', async () => {
+			const realisticMetadata = createRealisticMetadata();
+			const tasks: Task[] = [
+				createTask('1', {
+					title: 'Sync from GitHub',
+					metadata: realisticMetadata
+				})
+			];
+			await storage.saveTasks(tasks);
+
+			// AI enriches the task
+			await storage.updateTask('1', {
+				title: 'Implement user authentication',
+				description: 'Set up JWT-based authentication system',
+				details: `
+## Implementation Plan
+1. Create auth middleware
+2. Implement JWT token generation
+3. Add refresh token logic
+4. Set up protected routes
+				`.trim(),
+				testStrategy:
+					'Unit tests for JWT functions, integration tests for auth flow'
+			});
+
+			const loadedTasks = await storage.loadTasks();
+			// All AI updates applied
+			expect(loadedTasks[0].title).toBe('Implement user authentication');
+			expect(loadedTasks[0].details).toContain('Implementation Plan');
+			// Realistic metadata preserved with all its nested structure
+			expect(loadedTasks[0].metadata).toEqual(realisticMetadata);
+			expect(
+				(loadedTasks[0].metadata as Record<string, unknown>).githubIssue
+			).toBe(42);
+			expect(
+				(
+					(loadedTasks[0].metadata as Record<string, unknown>).jira as Record<
+						string,
+						unknown
+					>
+				).key
+			).toBe('PROJ-123');
+		});
+	});
+
+	describe('expand-task operation simulation', () => {
+		it('should preserve parent task metadata when adding AI-generated subtasks', async () => {
+			const parentMetadata = { tracked: true, source: 'import' };
+			const tasks: Task[] = [
+				createTask('1', {
+					metadata: parentMetadata,
+					subtasks: []
+				})
+			];
+			await storage.saveTasks(tasks);
+
+			// Simulate expand-task: AI generates subtasks (without metadata)
+			const aiGeneratedSubtasks: Subtask[] = [
+				{
+					id: 1,
+					parentId: '1',
+					title: 'AI Subtask 1',
+					description: 'First step generated by AI',
+					status: 'pending',
+					priority: 'medium',
+					dependencies: [],
+					details: 'Implementation details',
+					testStrategy: 'Test approach'
+					// No metadata - AI doesn't generate it
+				},
+				{
+					id: 2,
+					parentId: '1',
+					title: 'AI Subtask 2',
+					description: 'Second step generated by AI',
+					status: 'pending',
+					priority: 'medium',
+					dependencies: ['1'],
+					details: 'More details',
+					testStrategy: 'More tests'
+				}
+			];
+
+			// Apply subtasks update
+			await storage.updateTask('1', { subtasks: aiGeneratedSubtasks });
+
+			// Verify parent metadata preserved
+			const loadedTasks = await storage.loadTasks();
+			expect(loadedTasks[0].metadata).toEqual(parentMetadata);
+			expect(loadedTasks[0].subtasks).toHaveLength(2);
+			// Subtasks don't inherit parent metadata
+			expect(loadedTasks[0].subtasks[0].metadata).toBeUndefined();
+			expect(loadedTasks[0].subtasks[1].metadata).toBeUndefined();
+		});
+
+		it('should preserve subtask metadata when parent is updated', async () => {
+			const tasks: Task[] = [
+				createTask('1', {
+					metadata: { parentMeta: 'parent-value' },
+					subtasks: [
+						{
+							id: 1,
+							parentId: '1',
+							title: 'Subtask with metadata',
+							description: 'Has its own metadata',
+							status: 'pending',
+							priority: 'medium',
+							dependencies: [],
+							details: '',
+							testStrategy: '',
+							metadata: { subtaskMeta: 'subtask-value' }
+						}
+					]
+				})
+			];
+			await storage.saveTasks(tasks);
+
+			// AI updates parent task (not subtasks)
+			await storage.updateTask('1', {
+				title: 'Parent Updated by AI',
+				description: 'New description'
+			});
+
+			const loadedTasks = await storage.loadTasks();
+			// Parent metadata preserved
+			expect(loadedTasks[0].metadata).toEqual({ parentMeta: 'parent-value' });
+			// Subtask and its metadata preserved
+			expect(loadedTasks[0].subtasks[0].metadata).toEqual({
+				subtaskMeta: 'subtask-value'
+			});
+		});
+	});
+
+	describe('parse-prd operation simulation', () => {
+		it('should generate tasks without metadata field (as AI would)', async () => {
+			// Simulate parse-prd output: AI generates tasks without metadata
+			const aiGeneratedTasks: Task[] = [
+				{
+					id: '1',
+					title: 'Set up project structure',
+					description: 'Initialize the project with proper folder structure',
+					status: 'pending',
+					priority: 'high',
+					dependencies: [],
+					details: 'Create src/, tests/, docs/ directories',
+					testStrategy: 'Verify directories exist',
+					subtasks: []
+					// No metadata - AI doesn't generate it
+				},
+				{
+					id: '2',
+					title: 'Implement core functionality',
+					description: 'Build the main features',
+					status: 'pending',
+					priority: 'high',
+					dependencies: ['1'],
+					details: 'Implement main modules',
+					testStrategy: 'Unit tests for each module',
+					subtasks: []
+				}
+			];
+
+			await storage.saveTasks(aiGeneratedTasks);
+
+			// Verify tasks saved correctly without metadata
+			const loadedTasks = await storage.loadTasks();
+			expect(loadedTasks).toHaveLength(2);
+			expect(loadedTasks[0].metadata).toBeUndefined();
+			expect(loadedTasks[1].metadata).toBeUndefined();
+			// Later, user can add metadata
+			await storage.updateTask('1', {
+				metadata: { externalId: 'USER-ADDED-123' }
+			});
+			const updatedTasks = await storage.loadTasks();
+			expect(updatedTasks[0].metadata).toEqual({
+				externalId: 'USER-ADDED-123'
+			});
+		});
+	});
+
+	describe('update-subtask operation simulation', () => {
+		it('should preserve subtask metadata when appending info', async () => {
+			const tasks: Task[] = [
+				createTask('1', {
+					subtasks: [
+						{
+							id: 1,
+							parentId: '1',
+							title: 'Tracked subtask',
+							description: 'Has metadata from import',
+							status: 'pending',
+							priority: 'medium',
+							dependencies: [],
+							details: 'Initial details',
+							testStrategy: '',
+							metadata: { importedFrom: 'jira', ticketId: 'JIRA-456' }
+						}
+					]
+				})
+			];
+			await storage.saveTasks(tasks);
+
+			// Update subtask details (like update-subtask command does)
+			const updatedSubtask: Subtask = {
+				id: 1,
+				parentId: '1',
+				title: 'Tracked subtask',
+				description: 'Has metadata from import',
+				status: 'in-progress',
+				priority: 'medium',
+				dependencies: [],
+				details:
+					'Initial details\n\n<info added on 2024-01-20T10:00:00Z>\nImplementation notes from AI\n</info added on 2024-01-20T10:00:00Z>',
+				testStrategy: 'AI suggested tests',
+				metadata: { importedFrom: 'jira', ticketId: 'JIRA-456' }
+			};
+
+			await storage.updateTask('1', { subtasks: [updatedSubtask] });
+
+			const loadedTasks = await storage.loadTasks();
+			expect(loadedTasks[0].subtasks[0].metadata).toEqual({
+				importedFrom: 'jira',
+				ticketId: 'JIRA-456'
+			});
+			expect(loadedTasks[0].subtasks[0].details).toContain(
+				'Implementation notes from AI'
+			);
+		});
+	});
+
+	describe('mixed AI and storage metadata coexistence', () => {
+		it('should preserve user metadata alongside AI-generated task fields', async () => {
+			const tasks: Task[] = [
+				createTask('1', {
+					// AI-generated fields
+					relevantFiles: [
+						{
+							path: 'src/auth.ts',
+							description: 'Auth module',
+							action: 'modify'
+						}
+					],
+					category: 'development',
+					skills: ['TypeScript', 'Security'],
+					acceptanceCriteria: ['Tests pass', 'Code reviewed'],
+					// User-defined metadata (from import)
+					metadata: {
+						externalId: 'JIRA-789',
+						storyPoints: 5,
+						sprint: 'Sprint 10'
+					}
+				})
+			];
+			await storage.saveTasks(tasks);
+
+			// AI updates the task (doesn't touch metadata)
+			await storage.updateTask('1', {
+				relevantFiles: [
+					{ path: 'src/auth.ts', description: 'Auth module', action: 'modify' },
+					{
+						path: 'src/middleware.ts',
+						description: 'Added middleware',
+						action: 'create'
+					}
+				],
+				skills: ['TypeScript', 'Security', 'JWT']
+			});
+
+			const loadedTasks = await storage.loadTasks();
+			// AI fields updated
+			expect(loadedTasks[0].relevantFiles).toHaveLength(2);
+			expect(loadedTasks[0].skills).toContain('JWT');
+			// User metadata preserved
+			expect(loadedTasks[0].metadata).toEqual({
+				externalId: 'JIRA-789',
+				storyPoints: 5,
+				sprint: 'Sprint 10'
+			});
+		});
+	});
+
+	describe('edge cases for AI operations', () => {
+		it('should handle task with only metadata being updated by AI', async () => {
+			// Task has ONLY metadata set (sparse task)
+			const tasks: Task[] = [
+				createTask('1', {
+					metadata: { sparse: true, tracking: 'minimal' }
+				})
+			];
+			await storage.saveTasks(tasks);
+
+			// AI fills in all the other fields
+			await storage.updateTask('1', {
+				title: 'AI Generated Title',
+				description: 'AI Generated Description',
+				details: 'AI Generated Details',
+				testStrategy: 'AI Generated Test Strategy',
+				priority: 'high'
+			});
+
+			const loadedTasks = await storage.loadTasks();
+			expect(loadedTasks[0].title).toBe('AI Generated Title');
+			expect(loadedTasks[0].priority).toBe('high');
+			expect(loadedTasks[0].metadata).toEqual({
+				sparse: true,
+				tracking: 'minimal'
+			});
+		});
+
+		it('should preserve deeply nested metadata through AI operations', async () => {
+			const deepMetadata = {
+				integration: {
+					source: {
+						type: 'github',
+						repo: {
+							owner: 'org',
+							name: 'repo',
+							issue: {
+								number: 123,
+								labels: ['bug', 'priority-1']
+							}
+						}
+					}
+				}
+			};
+			const tasks: Task[] = [createTask('1', { metadata: deepMetadata })];
+			await storage.saveTasks(tasks);
+
+			// Multiple AI operations
+			await storage.updateTask('1', { title: 'Update 1' });
+			await storage.updateTask('1', { description: 'Update 2' });
+			await storage.updateTask('1', { status: 'in-progress' });
+
+			const loadedTasks = await storage.loadTasks();
+			expect(loadedTasks[0].metadata).toEqual(deepMetadata);
+		});
+	});
+});
--- a/packages/tm-core/tests/integration/mcp-tools/metadata-updates.test.ts
+++ b/packages/tm-core/tests/integration/mcp-tools/metadata-updates.test.ts
@@ -0,0 +1,540 @@
+/**
+ * @fileoverview Integration tests for MCP tool metadata updates
+ *
+ * Tests that metadata updates via update-task and update-subtask MCP tools
+ * work correctly with the TASK_MASTER_ALLOW_METADATA_UPDATES flag.
+ *
+ * These tests validate the metadata flow from MCP tool layer through
+ * direct functions to the legacy scripts and storage layer.
+ *
+ * NOTE: These tests focus on validation logic (JSON parsing, env flags, merge behavior)
+ * rather than full end-to-end MCP tool calls. End-to-end behavior is covered by:
+ * - FileStorage metadata tests (storage layer)
+ * - AI operation metadata preservation tests (full workflow)
+ * - Direct function integration (covered by the validation tests here)
+ */
+
+import { afterEach, beforeEach, describe, expect, it } from 'vitest';
+import * as fs from 'fs';
+import * as path from 'path';
+import * as os from 'os';
+import { validateMcpMetadata } from '@tm/mcp';
+
+describe('MCP Tool Metadata Updates - Integration Tests', () => {
+	let tempDir: string;
+	let tasksJsonPath: string;
+
+	beforeEach(() => {
+		// Create a temp directory for each test
+		tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'taskmaster-mcp-test-'));
+		// Create .taskmaster/tasks directory structure
+		const taskmasterDir = path.join(tempDir, '.taskmaster', 'tasks');
+		fs.mkdirSync(taskmasterDir, { recursive: true });
+		tasksJsonPath = path.join(taskmasterDir, 'tasks.json');
+	});
+
+	afterEach(() => {
+		// Clean up temp directory
+		fs.rmSync(tempDir, { recursive: true, force: true });
+		// Reset env vars
+		delete process.env.TASK_MASTER_ALLOW_METADATA_UPDATES;
+	});
+
+	describe('metadata JSON validation', () => {
+		it('should validate metadata is a valid JSON object', () => {
+			// Test valid JSON objects
+			const validMetadata = [
+				'{"key": "value"}',
+				'{"githubIssue": 42, "sprint": "Q1"}',
+				'{"nested": {"deep": true}}'
+			];
+
+			for (const meta of validMetadata) {
+				const parsed = JSON.parse(meta);
+				expect(typeof parsed).toBe('object');
+				expect(parsed).not.toBeNull();
+				expect(Array.isArray(parsed)).toBe(false);
+			}
+		});
+
+		it('should reject invalid metadata formats', () => {
+			const invalidMetadata = [
+				'"string"', // Just a string
+				'123', // Just a number
+				'true', // Just a boolean
+				'null', // Null
+				'[1, 2, 3]' // Array
+			];
+
+			for (const meta of invalidMetadata) {
+				const parsed = JSON.parse(meta);
+				const isValidObject =
+					typeof parsed === 'object' &&
+					parsed !== null &&
+					!Array.isArray(parsed);
+				expect(isValidObject).toBe(false);
+			}
+		});
+
+		it('should reject invalid JSON strings', () => {
+			const invalidJson = [
+				'{key: "value"}', // Missing quotes
+				"{'key': 'value'}", // Single quotes
+				'{"key": }' // Incomplete
+			];
+
+			for (const json of invalidJson) {
+				expect(() => JSON.parse(json)).toThrow();
+			}
+		});
+	});
+
+	describe('TASK_MASTER_ALLOW_METADATA_UPDATES flag', () => {
+		it('should block metadata updates when flag is not set', () => {
+			delete process.env.TASK_MASTER_ALLOW_METADATA_UPDATES;
+			const allowMetadataUpdates =
+				process.env.TASK_MASTER_ALLOW_METADATA_UPDATES === 'true';
+			expect(allowMetadataUpdates).toBe(false);
+		});
+
+		it('should block metadata updates when flag is set to false', () => {
+			process.env.TASK_MASTER_ALLOW_METADATA_UPDATES = 'false';
+			const allowMetadataUpdates =
+				process.env.TASK_MASTER_ALLOW_METADATA_UPDATES === 'true';
+			expect(allowMetadataUpdates).toBe(false);
+		});
+
+		it('should allow metadata updates when flag is set to true', () => {
+			process.env.TASK_MASTER_ALLOW_METADATA_UPDATES = 'true';
+			const allowMetadataUpdates =
+				process.env.TASK_MASTER_ALLOW_METADATA_UPDATES === 'true';
+			expect(allowMetadataUpdates).toBe(true);
+		});
+
+		it('should be case-sensitive (TRUE should not work)', () => {
+			process.env.TASK_MASTER_ALLOW_METADATA_UPDATES = 'TRUE';
+			const allowMetadataUpdates =
+				process.env.TASK_MASTER_ALLOW_METADATA_UPDATES === 'true';
+			expect(allowMetadataUpdates).toBe(false);
+		});
+	});
+
+	describe('metadata merge logic', () => {
+		it('should merge new metadata with existing metadata', () => {
+			const existingMetadata = { githubIssue: 42, sprint: 'Q1' };
+			const newMetadata = { storyPoints: 5, reviewed: true };
+
+			const merged = {
+				...(existingMetadata || {}),
+				...(newMetadata || {})
+			};
+
+			expect(merged).toEqual({
+				githubIssue: 42,
+				sprint: 'Q1',
+				storyPoints: 5,
+				reviewed: true
+			});
+		});
+
+		it('should override existing keys with new values', () => {
+			const existingMetadata = { githubIssue: 42, sprint: 'Q1' };
+			const newMetadata = { sprint: 'Q2' }; // Override sprint
+
+			const merged = {
+				...(existingMetadata || {}),
+				...(newMetadata || {})
+			};
+
+			expect(merged).toEqual({
+				githubIssue: 42,
+				sprint: 'Q2' // Overridden
+			});
+		});
+
+		it('should handle empty existing metadata', () => {
+			const existingMetadata = undefined;
+			const newMetadata = { key: 'value' };
+
+			const merged = {
+				...(existingMetadata || {}),
+				...(newMetadata || {})
+			};
+
+			expect(merged).toEqual({ key: 'value' });
+		});
+
+		it('should handle empty new metadata', () => {
+			const existingMetadata = { key: 'value' };
+			const newMetadata = undefined;
+
+			const merged = {
+				...(existingMetadata || {}),
+				...(newMetadata || {})
+			};
+
+			expect(merged).toEqual({ key: 'value' });
+		});
+
+		it('should preserve nested objects in metadata', () => {
+			const existingMetadata = {
+				jira: { key: 'PROJ-123' },
+				other: 'data'
+			};
+			const newMetadata = {
+				jira: { key: 'PROJ-456', type: 'bug' } // Replace entire jira object
+			};
+
+			const merged = {
+				...(existingMetadata || {}),
+				...(newMetadata || {})
+			};
+
+			expect(merged).toEqual({
+				jira: { key: 'PROJ-456', type: 'bug' }, // Entire jira object replaced
+				other: 'data'
+			});
+		});
+	});
+
+	describe('metadata-only update detection', () => {
+		it('should detect metadata-only update when prompt is empty', () => {
+			const prompt: string = '';
+			const metadata = { key: 'value' };
+
+			const isMetadataOnly = metadata && (!prompt || prompt.trim() === '');
+			expect(isMetadataOnly).toBe(true);
+		});
+
+		it('should detect metadata-only update when prompt is whitespace', () => {
+			const prompt: string = '   ';
+			const metadata = { key: 'value' };
+
+			const isMetadataOnly = metadata && (!prompt || prompt.trim() === '');
+			expect(isMetadataOnly).toBe(true);
+		});
+
+		it('should not be metadata-only when prompt is provided', () => {
+			const prompt: string = 'Update task details';
+			const metadata = { key: 'value' };
+
+			const isMetadataOnly = metadata && (!prompt || prompt.trim() === '');
+			expect(isMetadataOnly).toBe(false);
+		});
+
+		it('should not be metadata-only when neither is provided', () => {
+			const prompt: string = '';
+			const metadata = null;
+
+			const isMetadataOnly = metadata && (!prompt || prompt.trim() === '');
+			expect(isMetadataOnly).toBeFalsy(); // metadata is null, so falsy
+		});
+	});
+
+	describe('tasks.json file format with metadata', () => {
+		it('should write and read metadata correctly in tasks.json', () => {
+			const tasksData = {
+				tasks: [
+					{
+						id: 1,
+						title: 'Test Task',
+						description: 'Description',
+						status: 'pending',
+						priority: 'medium',
+						dependencies: [],
+						details: '',
+						testStrategy: '',
+						subtasks: [],
+						metadata: {
+							githubIssue: 42,
+							sprint: 'Q1-S3',
+							storyPoints: 5
+						}
+					}
+				],
+				metadata: {
+					version: '1.0.0',
+					lastModified: new Date().toISOString(),
+					taskCount: 1,
+					completedCount: 0
+				}
+			};
+
+			// Write
+			fs.writeFileSync(tasksJsonPath, JSON.stringify(tasksData, null, 2));
+
+			// Read and verify
+			const rawContent = fs.readFileSync(tasksJsonPath, 'utf-8');
+			const parsed = JSON.parse(rawContent);
+
+			expect(parsed.tasks[0].metadata).toEqual({
+				githubIssue: 42,
+				sprint: 'Q1-S3',
+				storyPoints: 5
+			});
+		});
+
+		it('should write and read subtask metadata correctly', () => {
+			const tasksData = {
+				tasks: [
+					{
+						id: 1,
+						title: 'Parent Task',
+						description: 'Description',
+						status: 'pending',
+						priority: 'medium',
+						dependencies: [],
+						details: '',
+						testStrategy: '',
+						subtasks: [
+							{
+								id: 1,
+								parentId: 1,
+								title: 'Subtask',
+								description: 'Subtask description',
+								status: 'pending',
+								priority: 'medium',
+								dependencies: [],
+								details: '',
+								testStrategy: '',
+								metadata: {
+									linkedTicket: 'JIRA-456',
+									reviewed: true
+								}
+							}
+						]
+					}
+				],
+				metadata: {
+					version: '1.0.0',
+					lastModified: new Date().toISOString(),
+					taskCount: 1,
+					completedCount: 0
+				}
+			};
+
+			// Write
+			fs.writeFileSync(tasksJsonPath, JSON.stringify(tasksData, null, 2));
+
+			// Read and verify
+			const rawContent = fs.readFileSync(tasksJsonPath, 'utf-8');
+			const parsed = JSON.parse(rawContent);
+
+			expect(parsed.tasks[0].subtasks[0].metadata).toEqual({
+				linkedTicket: 'JIRA-456',
+				reviewed: true
+			});
+		});
+	});
+
+	describe('error message formatting', () => {
+		it('should provide clear error for disabled metadata updates', () => {
+			const errorMessage =
+				'Metadata updates are disabled. Set TASK_MASTER_ALLOW_METADATA_UPDATES=true in your MCP server environment to enable metadata modifications.';
+
+			expect(errorMessage).toContain('TASK_MASTER_ALLOW_METADATA_UPDATES');
+			expect(errorMessage).toContain('true');
+			expect(errorMessage).toContain('MCP server environment');
+		});
+
+		it('should provide clear error for invalid JSON', () => {
+			const invalidJson = '{key: value}';
+			const errorMessage = `Invalid metadata JSON: ${invalidJson}. Provide a valid JSON object string.`;
+
+			expect(errorMessage).toContain(invalidJson);
+			expect(errorMessage).toContain('valid JSON object');
+		});
+
+		it('should provide clear error for non-object JSON', () => {
+			const errorMessage =
+				'Invalid metadata: must be a JSON object (not null or array)';
+
+			expect(errorMessage).toContain('JSON object');
+			expect(errorMessage).toContain('not null or array');
+		});
+	});
+});
+
+/**
+ * Unit tests for the actual validateMcpMetadata function from @tm/mcp
+ * These tests verify the security gate behavior for MCP metadata updates.
+ */
+describe('validateMcpMetadata function', () => {
+	// Mock error response creator that matches the MCP ContentResult format
+	const mockCreateErrorResponse = (message: string) => ({
+		content: [{ type: 'text' as const, text: `Error: ${message}` }],
+		isError: true
+	});
+
+	// Helper to safely extract text from content
+	const getErrorText = (
+		error: { content: Array<{ type: string; text?: string }> } | undefined
+	): string => {
+		if (!error?.content?.[0]) return '';
+		const content = error.content[0];
+		return 'text' in content ? (content.text ?? '') : '';
+	};
+
+	afterEach(() => {
+		delete process.env.TASK_MASTER_ALLOW_METADATA_UPDATES;
+	});
+
+	describe('when metadataString is null/undefined', () => {
+		it('should return null parsedMetadata for undefined input', () => {
+			const result = validateMcpMetadata(undefined, mockCreateErrorResponse);
+			expect(result.parsedMetadata).toBeNull();
+			expect(result.error).toBeUndefined();
+		});
+
+		it('should return null parsedMetadata for null input', () => {
+			const result = validateMcpMetadata(null, mockCreateErrorResponse);
+			expect(result.parsedMetadata).toBeNull();
+			expect(result.error).toBeUndefined();
+		});
+
+		it('should return null parsedMetadata for empty string', () => {
+			const result = validateMcpMetadata('', mockCreateErrorResponse);
+			expect(result.parsedMetadata).toBeNull();
+			expect(result.error).toBeUndefined();
+		});
+	});
+
+	describe('when TASK_MASTER_ALLOW_METADATA_UPDATES is not set', () => {
+		beforeEach(() => {
+			delete process.env.TASK_MASTER_ALLOW_METADATA_UPDATES;
+		});
+
+		it('should return error when flag is not set', () => {
+			const result = validateMcpMetadata(
+				'{"key": "value"}',
+				mockCreateErrorResponse
+			);
+			expect(result.error).toBeDefined();
+			expect(result.error?.isError).toBe(true);
+			expect(getErrorText(result.error)).toContain(
+				'TASK_MASTER_ALLOW_METADATA_UPDATES'
+			);
+		});
+
+		it('should return error when flag is set to "false"', () => {
+			process.env.TASK_MASTER_ALLOW_METADATA_UPDATES = 'false';
+			const result = validateMcpMetadata(
+				'{"key": "value"}',
+				mockCreateErrorResponse
+			);
+			expect(result.error).toBeDefined();
+			expect(result.error?.isError).toBe(true);
+		});
+
+		it('should return error when flag is "TRUE" (case sensitive)', () => {
+			process.env.TASK_MASTER_ALLOW_METADATA_UPDATES = 'TRUE';
+			const result = validateMcpMetadata(
+				'{"key": "value"}',
+				mockCreateErrorResponse
+			);
+			expect(result.error).toBeDefined();
+			expect(result.error?.isError).toBe(true);
+		});
+
+		it('should return error when flag is "True" (case sensitive)', () => {
+			process.env.TASK_MASTER_ALLOW_METADATA_UPDATES = 'True';
+			const result = validateMcpMetadata(
+				'{"key": "value"}',
+				mockCreateErrorResponse
+			);
+			expect(result.error).toBeDefined();
+			expect(result.error?.isError).toBe(true);
+		});
+	});
+
+	describe('when TASK_MASTER_ALLOW_METADATA_UPDATES is "true"', () => {
+		beforeEach(() => {
+			process.env.TASK_MASTER_ALLOW_METADATA_UPDATES = 'true';
+		});
+
+		it('should return parsed metadata for valid JSON object', () => {
+			const result = validateMcpMetadata(
+				'{"key": "value"}',
+				mockCreateErrorResponse
+			);
+			expect(result.parsedMetadata).toEqual({ key: 'value' });
+			expect(result.error).toBeUndefined();
+		});
+
+		it('should return parsed metadata for complex nested object', () => {
+			const complexMeta = {
+				githubIssue: 42,
+				sprint: 'Q1-S3',
+				nested: { deep: { value: true } },
+				array: [1, 2, 3]
+			};
+			const result = validateMcpMetadata(
+				JSON.stringify(complexMeta),
+				mockCreateErrorResponse
+			);
+			expect(result.parsedMetadata).toEqual(complexMeta);
+			expect(result.error).toBeUndefined();
+		});
+
+		it('should return parsed metadata for empty object', () => {
+			const result = validateMcpMetadata('{}', mockCreateErrorResponse);
+			expect(result.parsedMetadata).toEqual({});
+			expect(result.error).toBeUndefined();
+		});
+
+		it('should return error for invalid JSON string', () => {
+			const result = validateMcpMetadata(
+				'{key: "value"}',
+				mockCreateErrorResponse
+			);
+			expect(result.error).toBeDefined();
+			expect(result.error?.isError).toBe(true);
+			expect(getErrorText(result.error)).toContain('Invalid metadata JSON');
+		});
+
+		it('should return error for JSON array', () => {
+			const result = validateMcpMetadata('[1, 2, 3]', mockCreateErrorResponse);
+			expect(result.error).toBeDefined();
+			expect(result.error?.isError).toBe(true);
+			expect(getErrorText(result.error)).toContain(
+				'must be a JSON object (not null or array)'
+			);
+		});
+
+		it('should return error for JSON null', () => {
+			const result = validateMcpMetadata('null', mockCreateErrorResponse);
+			expect(result.error).toBeDefined();
+			expect(result.error?.isError).toBe(true);
+			expect(getErrorText(result.error)).toContain(
+				'must be a JSON object (not null or array)'
+			);
+		});
+
+		it('should return error for JSON string primitive', () => {
+			const result = validateMcpMetadata('"string"', mockCreateErrorResponse);
+			expect(result.error).toBeDefined();
+			expect(result.error?.isError).toBe(true);
+			expect(getErrorText(result.error)).toContain(
+				'must be a JSON object (not null or array)'
+			);
+		});
+
+		it('should return error for JSON number primitive', () => {
+			const result = validateMcpMetadata('123', mockCreateErrorResponse);
+			expect(result.error).toBeDefined();
+			expect(result.error?.isError).toBe(true);
+			expect(getErrorText(result.error)).toContain(
+				'must be a JSON object (not null or array)'
+			);
+		});
+
+		it('should return error for JSON boolean primitive', () => {
+			const result = validateMcpMetadata('true', mockCreateErrorResponse);
+			expect(result.error).toBeDefined();
+			expect(result.error?.isError).toBe(true);
+			expect(getErrorText(result.error)).toContain(
+				'must be a JSON object (not null or array)'
+			);
+		});
+	});
+});
--- a/packages/tm-core/tests/integration/storage/file-storage-metadata.test.ts
+++ b/packages/tm-core/tests/integration/storage/file-storage-metadata.test.ts
@@ -0,0 +1,472 @@
+/**
+ * @fileoverview Integration tests for FileStorage metadata preservation
+ *
+ * Tests that user-defined metadata survives all FileStorage CRUD operations
+ * including load, save, update, and append.
+ */
+
+import { afterEach, beforeEach, describe, expect, it } from 'vitest';
+import * as fs from 'fs';
+import * as path from 'path';
+import * as os from 'os';
+import { FileStorage } from '../../../src/modules/storage/adapters/file-storage/file-storage.js';
+import type { Task } from '../../../src/common/types/index.js';
+
+/**
+ * Creates a minimal valid task for testing
+ */
+function createTask(id: string, overrides: Partial<Task> = {}): Task {
+	return {
+		id,
+		title: `Task ${id}`,
+		description: `Description for task ${id}`,
+		status: 'pending',
+		priority: 'medium',
+		dependencies: [],
+		details: '',
+		testStrategy: '',
+		subtasks: [],
+		...overrides
+	};
+}
+
+describe('FileStorage Metadata Preservation - Integration Tests', () => {
+	let tempDir: string;
+	let storage: FileStorage;
+
+	beforeEach(() => {
+		// Create a temp directory for each test
+		tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'taskmaster-test-'));
+		// Create .taskmaster/tasks directory structure
+		const taskmasterDir = path.join(tempDir, '.taskmaster', 'tasks');
+		fs.mkdirSync(taskmasterDir, { recursive: true });
+		storage = new FileStorage(tempDir);
+	});
+
+	afterEach(() => {
+		// Clean up temp directory
+		fs.rmSync(tempDir, { recursive: true, force: true });
+	});
+
+	describe('saveTasks() and loadTasks() round-trip', () => {
+		it('should preserve metadata through save and load cycle', async () => {
+			const tasks: Task[] = [
+				createTask('1', {
+					metadata: {
+						externalId: 'JIRA-123',
+						source: 'import',
+						customField: { nested: 'value' }
+					}
+				}),
+				createTask('2', {
+					metadata: {
+						score: 85,
+						isUrgent: true
+					}
+				})
+			];
+
+			await storage.saveTasks(tasks);
+			const loadedTasks = await storage.loadTasks();
+
+			expect(loadedTasks).toHaveLength(2);
+			expect(loadedTasks[0].metadata).toEqual({
+				externalId: 'JIRA-123',
+				source: 'import',
+				customField: { nested: 'value' }
+			});
+			expect(loadedTasks[1].metadata).toEqual({
+				score: 85,
+				isUrgent: true
+			});
+		});
+
+		it('should preserve empty metadata object', async () => {
+			const tasks: Task[] = [createTask('1', { metadata: {} })];
+
+			await storage.saveTasks(tasks);
+			const loadedTasks = await storage.loadTasks();
+
+			expect(loadedTasks[0].metadata).toEqual({});
+		});
+
+		it('should handle tasks without metadata', async () => {
+			const tasks: Task[] = [createTask('1')]; // No metadata
+
+			await storage.saveTasks(tasks);
+			const loadedTasks = await storage.loadTasks();
+
+			expect(loadedTasks[0].metadata).toBeUndefined();
+		});
+
+		it('should preserve complex metadata with various types', async () => {
+			const complexMetadata = {
+				string: 'value',
+				number: 42,
+				float: 3.14,
+				boolean: true,
+				nullValue: null,
+				array: [1, 'two', { three: 3 }],
+				nested: {
+					deep: {
+						deeper: {
+							value: 'found'
+						}
+					}
+				}
+			};
+
+			const tasks: Task[] = [createTask('1', { metadata: complexMetadata })];
+
+			await storage.saveTasks(tasks);
+			const loadedTasks = await storage.loadTasks();
+
+			expect(loadedTasks[0].metadata).toEqual(complexMetadata);
+		});
+
+		it('should preserve metadata on subtasks', async () => {
+			const tasks: Task[] = [
+				createTask('1', {
+					metadata: { parentMeta: 'value' },
+					subtasks: [
+						{
+							id: 1,
+							parentId: '1',
+							title: 'Subtask 1',
+							description: 'Description',
+							status: 'pending',
+							priority: 'medium',
+							dependencies: [],
+							details: '',
+							testStrategy: '',
+							metadata: { subtaskMeta: 'subtask-value' }
+						}
+					]
+				})
+			];
+
+			await storage.saveTasks(tasks);
+			const loadedTasks = await storage.loadTasks();
+
+			expect(loadedTasks[0].metadata).toEqual({ parentMeta: 'value' });
+			expect(loadedTasks[0].subtasks[0].metadata).toEqual({
+				subtaskMeta: 'subtask-value'
+			});
+		});
+	});
+
+	describe('updateTask() metadata preservation', () => {
+		it('should preserve existing metadata when updating other fields', async () => {
+			const originalMetadata = { externalId: 'EXT-123', version: 1 };
+			const tasks: Task[] = [createTask('1', { metadata: originalMetadata })];
+
+			await storage.saveTasks(tasks);
+
+			// Update title only, not metadata
+			await storage.updateTask('1', { title: 'Updated Title' });
+
+			const loadedTasks = await storage.loadTasks();
+			expect(loadedTasks[0].title).toBe('Updated Title');
+			expect(loadedTasks[0].metadata).toEqual(originalMetadata);
+		});
+
+		it('should allow updating metadata field directly', async () => {
+			const tasks: Task[] = [createTask('1', { metadata: { original: true } })];
+
+			await storage.saveTasks(tasks);
+
+			// Update metadata
+			await storage.updateTask('1', {
+				metadata: { original: true, updated: true, newField: 'value' }
+			});
+
+			const loadedTasks = await storage.loadTasks();
+			expect(loadedTasks[0].metadata).toEqual({
+				original: true,
+				updated: true,
+				newField: 'value'
+			});
+		});
+
+		it('should allow replacing metadata entirely', async () => {
+			const tasks: Task[] = [
+				createTask('1', { metadata: { oldField: 'old' } })
+			];
+
+			await storage.saveTasks(tasks);
+
+			// Replace metadata entirely
+			await storage.updateTask('1', { metadata: { newField: 'new' } });
+
+			const loadedTasks = await storage.loadTasks();
+			expect(loadedTasks[0].metadata).toEqual({ newField: 'new' });
+		});
+
+		it('should preserve metadata when updating status', async () => {
+			const tasks: Task[] = [createTask('1', { metadata: { tracked: true } })];
+
+			await storage.saveTasks(tasks);
+			await storage.updateTask('1', { status: 'in-progress' });
+
+			const loadedTasks = await storage.loadTasks();
+			expect(loadedTasks[0].status).toBe('in-progress');
+			expect(loadedTasks[0].metadata).toEqual({ tracked: true });
+		});
+	});
+
+	describe('appendTasks() metadata preservation', () => {
+		it('should preserve metadata on existing tasks when appending', async () => {
+			const existingTasks: Task[] = [
+				createTask('1', { metadata: { existing: true } })
+			];
+
+			await storage.saveTasks(existingTasks);
+
+			// Append new tasks
+			const newTasks: Task[] = [
+				createTask('2', { metadata: { newTask: true } })
+			];
+
+			await storage.appendTasks(newTasks);
+
+			const loadedTasks = await storage.loadTasks();
+			expect(loadedTasks).toHaveLength(2);
+			expect(loadedTasks.find((t) => t.id === '1')?.metadata).toEqual({
+				existing: true
+			});
+			expect(loadedTasks.find((t) => t.id === '2')?.metadata).toEqual({
+				newTask: true
+			});
+		});
+	});
+
+	describe('loadTask() single task metadata', () => {
+		it('should preserve metadata when loading single task', async () => {
+			const tasks: Task[] = [
+				createTask('1', { metadata: { specific: 'metadata' } }),
+				createTask('2', { metadata: { other: 'data' } })
+			];
+
+			await storage.saveTasks(tasks);
+			const task = await storage.loadTask('1');
+
+			expect(task).toBeDefined();
+			expect(task?.metadata).toEqual({ specific: 'metadata' });
+		});
+	});
+
+	describe('metadata alongside AI implementation metadata', () => {
+		it('should preserve both user metadata and AI metadata', async () => {
+			const tasks: Task[] = [
+				createTask('1', {
+					// AI implementation metadata
+					relevantFiles: [
+						{
+							path: 'src/test.ts',
+							description: 'Test file',
+							action: 'modify'
+						}
+					],
+					category: 'development',
+					skills: ['TypeScript'],
+					acceptanceCriteria: ['Tests pass'],
+					// User-defined metadata
+					metadata: {
+						externalId: 'JIRA-456',
+						importedAt: '2024-01-15T10:00:00Z'
+					}
+				})
+			];
+
+			await storage.saveTasks(tasks);
+			const loadedTasks = await storage.loadTasks();
+
+			// AI metadata preserved
+			expect(loadedTasks[0].relevantFiles).toHaveLength(1);
+			expect(loadedTasks[0].category).toBe('development');
+			expect(loadedTasks[0].skills).toEqual(['TypeScript']);
+
+			// User metadata preserved
+			expect(loadedTasks[0].metadata).toEqual({
+				externalId: 'JIRA-456',
+				importedAt: '2024-01-15T10:00:00Z'
+			});
+		});
+	});
+
+	describe('AI operation metadata preservation', () => {
+		it('should preserve metadata when updating task with AI-like partial update', async () => {
+			// Simulate existing task with user metadata
+			const tasks: Task[] = [
+				createTask('1', {
+					title: 'Original Title',
+					metadata: { externalId: 'JIRA-123', version: 1 }
+				})
+			];
+
+			await storage.saveTasks(tasks);
+
+			// Simulate AI update - only updates specific fields, no metadata field
+			// This mimics what happens when AI processes update-task
+			const aiUpdate: Partial<Task> = {
+				title: 'AI Updated Title',
+				description: 'AI generated description',
+				details: 'AI generated details'
+				// Note: no metadata field - AI schemas don't include it
+			};
+
+			await storage.updateTask('1', aiUpdate);
+
+			const loadedTasks = await storage.loadTasks();
+			expect(loadedTasks[0].title).toBe('AI Updated Title');
+			expect(loadedTasks[0].description).toBe('AI generated description');
+			// User metadata must be preserved
+			expect(loadedTasks[0].metadata).toEqual({
+				externalId: 'JIRA-123',
+				version: 1
+			});
+		});
+
+		it('should preserve metadata when adding AI-generated subtasks', async () => {
+			const tasks: Task[] = [
+				createTask('1', {
+					metadata: { tracked: true, source: 'import' },
+					subtasks: []
+				})
+			];
+
+			await storage.saveTasks(tasks);
+
+			// Simulate expand-task adding subtasks
+			// Subtasks from AI don't have metadata field
+			const updatedTask: Partial<Task> = {
+				subtasks: [
+					{
+						id: 1,
+						parentId: '1',
+						title: 'AI Generated Subtask',
+						description: 'Description',
+						status: 'pending',
+						priority: 'medium',
+						dependencies: [],
+						details: 'Details',
+						testStrategy: 'Tests'
+						// No metadata - AI doesn't generate it
+					}
+				]
+			};
+
+			await storage.updateTask('1', updatedTask);
+
+			const loadedTasks = await storage.loadTasks();
+			// Parent task metadata preserved
+			expect(loadedTasks[0].metadata).toEqual({
+				tracked: true,
+				source: 'import'
+			});
+			// Subtask has no metadata (as expected from AI)
+			expect(loadedTasks[0].subtasks[0].metadata).toBeUndefined();
+		});
+
+		it('should handle multiple sequential AI updates preserving metadata', async () => {
+			const tasks: Task[] = [
+				createTask('1', {
+					metadata: { originalField: 'preserved' }
+				})
+			];
+
+			await storage.saveTasks(tasks);
+
+			// First AI update
+			await storage.updateTask('1', { title: 'First Update' });
+			// Second AI update
+			await storage.updateTask('1', { description: 'Second Update' });
+			// Third AI update
+			await storage.updateTask('1', { priority: 'high' });
+
+			const loadedTasks = await storage.loadTasks();
+			expect(loadedTasks[0].title).toBe('First Update');
+			expect(loadedTasks[0].description).toBe('Second Update');
+			expect(loadedTasks[0].priority).toBe('high');
+			// Metadata preserved through all updates
+			expect(loadedTasks[0].metadata).toEqual({ originalField: 'preserved' });
+		});
+
+		it('should preserve metadata when update object omits metadata field entirely', async () => {
+			// This is how AI operations work - they simply don't include metadata
+			const tasks: Task[] = [
+				createTask('1', {
+					metadata: { important: 'data' }
+				})
+			];
+
+			await storage.saveTasks(tasks);
+
+			// Update WITHOUT metadata field (AI schemas don't include it)
+			const updateWithoutMetadata: Partial<Task> = { title: 'Updated' };
+			await storage.updateTask('1', updateWithoutMetadata);
+
+			const loadedTasks = await storage.loadTasks();
+			// When metadata field is absent from updates, existing metadata is preserved
+			expect(loadedTasks[0].metadata).toEqual({ important: 'data' });
+		});
+	});
+
+	describe('file format verification', () => {
+		it('should write metadata to JSON file correctly', async () => {
+			const tasks: Task[] = [createTask('1', { metadata: { written: true } })];
+
+			await storage.saveTasks(tasks);
+
+			// Read raw file to verify format
+			const filePath = path.join(tempDir, '.taskmaster', 'tasks', 'tasks.json');
+			const rawContent = fs.readFileSync(filePath, 'utf-8');
+			const parsed = JSON.parse(rawContent);
+
+			expect(parsed.tasks[0].metadata).toEqual({ written: true });
+		});
+
+		it('should load metadata from pre-existing JSON file', async () => {
+			// Write a tasks.json file manually
+			const tasksDir = path.join(tempDir, '.taskmaster', 'tasks');
+			const filePath = path.join(tasksDir, 'tasks.json');
+
+			const fileContent = {
+				tasks: [
+					{
+						id: '1',
+						title: 'Pre-existing task',
+						description: 'Description',
+						status: 'pending',
+						priority: 'medium',
+						dependencies: [],
+						details: '',
+						testStrategy: '',
+						subtasks: [],
+						metadata: {
+							preExisting: true,
+							importedFrom: 'external-system'
+						}
+					}
+				],
+				metadata: {
+					version: '1.0.0',
+					lastModified: new Date().toISOString(),
+					taskCount: 1,
+					completedCount: 0
+				}
+			};
+
+			fs.writeFileSync(filePath, JSON.stringify(fileContent, null, 2));
+
+			// Load through FileStorage
+			const loadedTasks = await storage.loadTasks();
+
+			expect(loadedTasks).toHaveLength(1);
+			expect(loadedTasks[0].metadata).toEqual({
+				preExisting: true,
+				importedFrom: 'external-system'
+			});
+		});
+	});
+});
--- a/packages/tm-core/tests/integration/storage/task-metadata-extraction.test.ts
+++ b/packages/tm-core/tests/integration/storage/task-metadata-extraction.test.ts
@@ -492,4 +492,157 @@ describe('Task Metadata Extraction - Integration Tests', () => {
 			expect(validCategories).toContain(task.category);
 		});
 	});
+
+	describe('User-Defined Metadata Field', () => {
+		it('should preserve user-defined metadata through JSON serialization', () => {
+			const taskWithMetadata: Task = {
+				id: '1',
+				title: 'Task with custom metadata',
+				description: 'Test description',
+				status: 'pending',
+				priority: 'high',
+				dependencies: [],
+				details: '',
+				testStrategy: '',
+				subtasks: [],
+				metadata: {
+					externalId: 'JIRA-123',
+					source: 'import',
+					customField: { nested: 'value' }
+				}
+			};
+
+			const serialized = JSON.stringify(taskWithMetadata);
+			const deserialized: Task = JSON.parse(serialized);
+
+			expect(deserialized.metadata).toEqual(taskWithMetadata.metadata);
+			expect(deserialized.metadata?.externalId).toBe('JIRA-123');
+			expect(deserialized.metadata?.customField).toEqual({ nested: 'value' });
+		});
+
+		it('should preserve metadata on subtasks through JSON serialization', () => {
+			const taskWithSubtasks: Task = {
+				id: '1',
+				title: 'Parent task',
+				description: 'Test',
+				status: 'pending',
+				priority: 'medium',
+				dependencies: [],
+				details: '',
+				testStrategy: '',
+				metadata: { parentMeta: true },
+				subtasks: [
+					{
+						id: 1,
+						parentId: '1',
+						title: 'Subtask 1',
+						description: 'Test',
+						status: 'pending',
+						priority: 'medium',
+						dependencies: [],
+						details: '',
+						testStrategy: '',
+						metadata: { subtaskMeta: 'value1' }
+					}
+				]
+			};
+
+			const serialized = JSON.stringify(taskWithSubtasks);
+			const deserialized: Task = JSON.parse(serialized);
+
+			expect(deserialized.metadata).toEqual({ parentMeta: true });
+			expect(deserialized.subtasks[0].metadata).toEqual({
+				subtaskMeta: 'value1'
+			});
+		});
+
+		it('should handle empty metadata object', () => {
+			const task: Task = {
+				id: '1',
+				title: 'Task',
+				description: 'Test',
+				status: 'pending',
+				priority: 'medium',
+				dependencies: [],
+				details: '',
+				testStrategy: '',
+				subtasks: [],
+				metadata: {}
+			};
+
+			const serialized = JSON.stringify(task);
+			const deserialized: Task = JSON.parse(serialized);
+
+			expect(deserialized.metadata).toEqual({});
+		});
+
+		it('should handle complex metadata with various types', () => {
+			const task: Task = {
+				id: '1',
+				title: 'Task',
+				description: 'Test',
+				status: 'pending',
+				priority: 'medium',
+				dependencies: [],
+				details: '',
+				testStrategy: '',
+				subtasks: [],
+				metadata: {
+					string: 'value',
+					number: 42,
+					boolean: true,
+					nullValue: null,
+					array: [1, 2, 3],
+					nested: {
+						deep: {
+							value: 'found'
+						}
+					}
+				}
+			};
+
+			const serialized = JSON.stringify(task);
+			const deserialized: Task = JSON.parse(serialized);
+
+			expect(deserialized.metadata?.string).toBe('value');
+			expect(deserialized.metadata?.number).toBe(42);
+			expect(deserialized.metadata?.boolean).toBe(true);
+			expect(deserialized.metadata?.nullValue).toBeNull();
+			expect(deserialized.metadata?.array).toEqual([1, 2, 3]);
+			expect((deserialized.metadata?.nested as any)?.deep?.value).toBe('found');
+		});
+
+		it('should preserve metadata alongside AI implementation metadata', () => {
+			const task: Task = {
+				id: '1',
+				title: 'Task',
+				description: 'Test',
+				status: 'pending',
+				priority: 'medium',
+				dependencies: [],
+				details: 'Some details',
+				testStrategy: 'Unit tests',
+				subtasks: [],
+				// AI implementation metadata
+				relevantFiles: [
+					{ path: 'src/test.ts', description: 'Test file', action: 'modify' }
+				],
+				category: 'development',
+				skills: ['TypeScript'],
+				// User-defined metadata
+				metadata: {
+					externalId: 'EXT-456',
+					importedAt: '2024-01-15T10:00:00Z'
+				}
+			};
+
+			const serialized = JSON.stringify(task);
+			const deserialized: Task = JSON.parse(serialized);
+
+			// Both types of metadata should be preserved
+			expect(deserialized.relevantFiles).toHaveLength(1);
+			expect(deserialized.category).toBe('development');
+			expect(deserialized.metadata?.externalId).toBe('EXT-456');
+		});
+	});
 });
--- a/scripts/modules/task-manager/update-subtask-by-id.js
+++ b/scripts/modules/task-manager/update-subtask-by-id.js
@@ -48,7 +48,13 @@ async function updateSubtaskById(
 	context = {},
 	outputFormat = context.mcpLog ? 'json' : 'text'
 ) {
-	const { session, mcpLog, projectRoot: providedProjectRoot, tag } = context;
+	const {
+		session,
+		mcpLog,
+		projectRoot: providedProjectRoot,
+		tag,
+		metadata
+	} = context;
 	const logFn = mcpLog || consoleLog;
 	const isMCP = !!mcpLog;

@@ -71,10 +77,13 @@ async function updateSubtaskById(
 		if (!subtaskId || typeof subtaskId !== 'string') {
 			throw new Error('Subtask ID cannot be empty.');
 		}
-
-		if (!prompt || typeof prompt !== 'string' || prompt.trim() === '') {
+		// Allow metadata-only updates (no prompt required if metadata is provided)
+		if (
+			(!prompt || typeof prompt !== 'string' || prompt.trim() === '') &&
+			!metadata
+		) {
 			throw new Error(
-				'Prompt cannot be empty. Please provide context for the subtask update.'
+				'Prompt cannot be empty unless metadata is provided. Please provide context for the subtask update or metadata to merge.'
 			);
 		}

@@ -93,6 +102,7 @@ async function updateSubtaskById(
 			tag,
 			appendMode: true, // Subtask updates are always append mode
 			useResearch,
+			metadata,
 			isMCP,
 			outputFormat,
 			report
@@ -164,6 +174,30 @@ async function updateSubtaskById(

 		const subtask = parentTask.subtasks[subtaskIndex];

+		// --- Metadata-Only Update (Fast Path) ---
+		// If only metadata is provided (no prompt), skip AI and just update metadata
+		if (metadata && (!prompt || prompt.trim() === '')) {
+			report('info', `Metadata-only update for subtask ${subtaskId}`);
+			// Merge new metadata with existing
+			subtask.metadata = {
+				...(subtask.metadata || {}),
+				...metadata
+			};
+			parentTask.subtasks[subtaskIndex] = subtask;
+			writeJSON(tasksPath, data, projectRoot, tag);
+			report(
+				'success',
+				`Successfully updated metadata for subtask ${subtaskId}`
+			);
+
+			return {
+				updatedSubtask: subtask,
+				telemetryData: null,
+				tagInfo: { tag }
+			};
+		}
+		// --- End Metadata-Only Update ---
+
 		// --- Context Gathering ---
 		let gatheredContext = '';
 		try {
@@ -334,6 +368,14 @@ async function updateSubtaskById(

 		const updatedSubtask = parentTask.subtasks[subtaskIndex];

+		// Merge metadata if provided (preserve existing metadata)
+		if (metadata) {
+			updatedSubtask.metadata = {
+				...(updatedSubtask.metadata || {}),
+				...metadata
+			};
+		}
+
 		if (outputFormat === 'text' && getDebugFlag(session)) {
 			console.log(
 				'>>> DEBUG: Subtask details AFTER AI update:',
--- a/scripts/modules/task-manager/update-task-by-id.js
+++ b/scripts/modules/task-manager/update-task-by-id.js
@@ -58,7 +58,13 @@ async function updateTaskById(
 	outputFormat = 'text',
 	appendMode = false
 ) {
-	const { session, mcpLog, projectRoot: providedProjectRoot, tag } = context;
+	const {
+		session,
+		mcpLog,
+		projectRoot: providedProjectRoot,
+		tag,
+		metadata
+	} = context;
 	const { report, isMCP } = createBridgeLogger(mcpLog, session);

 	try {
@@ -70,8 +76,15 @@ async function updateTaskById(
 		if (taskId === null || taskId === undefined || String(taskId).trim() === '')
 			throw new Error('Task ID cannot be empty.');

-		if (!prompt || typeof prompt !== 'string' || prompt.trim() === '')
-			throw new Error('Prompt cannot be empty.');
+		// Allow metadata-only updates (prompt can be empty if metadata is provided)
+		if (
+			(!prompt || typeof prompt !== 'string' || prompt.trim() === '') &&
+			!metadata
+		) {
+			throw new Error(
+				'Prompt cannot be empty unless metadata is provided for update.'
+			);
+		}

 		// Determine project root first (needed for API key checks)
 		const projectRoot = providedProjectRoot || findProjectRoot();
@@ -99,6 +112,7 @@ async function updateTaskById(
 			tag,
 			appendMode,
 			useResearch,
+			metadata,
 			isMCP,
 			outputFormat,
 			report
@@ -166,6 +180,27 @@ async function updateTaskById(
 		}
 		// --- End Task Loading ---

+		// --- Metadata-Only Update (Fast Path) ---
+		// If only metadata is provided (no prompt), skip AI and just update metadata
+		if (metadata && (!prompt || prompt.trim() === '')) {
+			report('info', `Metadata-only update for task ${taskId}`);
+			// Merge new metadata with existing
+			taskToUpdate.metadata = {
+				...(taskToUpdate.metadata || {}),
+				...metadata
+			};
+			data.tasks[taskIndex] = taskToUpdate;
+			writeJSON(tasksPath, data, projectRoot, tag);
+			report('success', `Successfully updated metadata for task ${taskId}`);
+
+			return {
+				updatedTask: taskToUpdate,
+				telemetryData: null,
+				tagInfo: { tag }
+			};
+		}
+		// --- End Metadata-Only Update ---
+
 		// --- Context Gathering ---
 		let gatheredContext = '';
 		try {
@@ -385,6 +420,14 @@ async function updateTaskById(
 					}
 				}

+				// Merge metadata if provided
+				if (metadata) {
+					taskToUpdate.metadata = {
+						...(taskToUpdate.metadata || {}),
+						...metadata
+					};
+				}
+
 				// Write the updated task back to file
 				data.tasks[taskIndex] = taskToUpdate;
 				writeJSON(tasksPath, data, projectRoot, tag);
@@ -455,6 +498,14 @@ async function updateTaskById(
 			if (updatedTask.subtasks && Array.isArray(updatedTask.subtasks)) {
 				let currentSubtaskId = 1;
 				updatedTask.subtasks = updatedTask.subtasks.map((subtask) => {
+					// Find original subtask to preserve its metadata
+					// Use type-coerced ID matching (AI may return string IDs vs numeric)
+					// Also match by title as fallback (subtask titles are typically unique)
+					const originalSubtask = taskToUpdate.subtasks?.find(
+						(st) =>
+							String(st.id) === String(subtask.id) ||
+							(subtask.title && st.title === subtask.title)
+					);
 					// Fix AI-generated subtask IDs that might be strings or use parent ID as prefix
 					const correctedSubtask = {
 						...subtask,
@@ -472,7 +523,11 @@ async function updateTaskById(
 									)
 							: [],
 						status: subtask.status || 'pending',
-						testStrategy: subtask.testStrategy ?? null
+						testStrategy: subtask.testStrategy ?? null,
+						// Preserve subtask metadata from original (AI schema excludes metadata)
+						...(originalSubtask?.metadata && {
+							metadata: originalSubtask.metadata
+						})
 					};
 					currentSubtaskId++;
 					return correctedSubtask;
@@ -529,6 +584,17 @@ async function updateTaskById(
 			}
 			// --- End Task Validation/Correction ---

+			// --- Preserve and Merge Metadata ---
+			// AI responses don't include metadata (AI schema excludes it)
+			// Preserve existing metadata from original task and merge new metadata if provided
+			if (taskToUpdate.metadata || metadata) {
+				updatedTask.metadata = {
+					...(taskToUpdate.metadata || {}),
+					...(metadata || {})
+				};
+			}
+			// --- End Preserve and Merge Metadata ---
+
 			// --- Update Task Data (Keep existing) ---
 			data.tasks[taskIndex] = updatedTask;
 			// --- End Update Task Data ---
--- a/src/schemas/base-schemas.js
+++ b/src/schemas/base-schemas.js
@@ -10,6 +10,11 @@ import { z } from 'zod';
 *
 * Other providers (Anthropic, Google, etc.) safely ignore this constraint.
 * See: https://platform.openai.com/docs/guides/structured-outputs
+ *
+ * NOTE: The `metadata` field (user-defined task metadata) is intentionally EXCLUDED
+ * from all AI schemas. This ensures AI operations cannot overwrite user metadata.
+ * When tasks are updated via AI, the spread operator preserves existing metadata
+ * since AI responses won't include a metadata field.
 */
 export const TaskStatusSchema = z.enum([
 	'pending',