diff --git a/apps/server/src/lib/settings-helpers.ts b/apps/server/src/lib/settings-helpers.ts
index 07564085..0cab0121 100644
--- a/apps/server/src/lib/settings-helpers.ts
+++ b/apps/server/src/lib/settings-helpers.ts
@@ -293,6 +293,29 @@ export async function getSkillsConfiguration(settingsService: SettingsService):
   };
 }
 
+/**
+ * Get Subagents configuration from settings.
+ * Returns configuration for enabling subagents and which sources to load from.
+ *
+ * @param settingsService - Settings service instance
+ * @returns Subagents configuration with enabled state, sources, and tool inclusion flag
+ */
+export async function getSubagentsConfiguration(settingsService: SettingsService): Promise<{
+  enabled: boolean;
+  sources: Array<'user' | 'project'>;
+  shouldIncludeInTools: boolean;
+}> {
+  const settings = await settingsService.getGlobalSettings();
+  const enabled = settings.enableSubagents ?? true; // Default enabled
+  const sources = settings.subagentsSources ?? ['user', 'project']; // Default both sources
+
+  return {
+    enabled,
+    sources,
+    shouldIncludeInTools: enabled && sources.length > 0,
+  };
+}
+
 /**
  * Get custom subagents from settings, merging global and project-level definitions.
  * Project-level subagents take precedence over global ones with the same name.
diff --git a/apps/server/src/providers/claude-provider.ts b/apps/server/src/providers/claude-provider.ts
index 5d033a3b..90defa72 100644
--- a/apps/server/src/providers/claude-provider.ts
+++ b/apps/server/src/providers/claude-provider.ts
@@ -72,17 +72,10 @@ export class ClaudeProvider extends BaseProvider {
     // Build Claude SDK options
     // AUTONOMOUS MODE: Always bypass permissions for fully autonomous operation
     const hasMcpServers = options.mcpServers && Object.keys(options.mcpServers).length > 0;
-    const defaultTools = [
-      'Read',
-      'Write',
-      'Edit',
-      'Glob',
-      'Grep',
-      'Bash',
-      'WebSearch',
-      'WebFetch',
-      'Skill',
-    ];
+    // Base tools available to all agents
+    // Note: 'Skill' and 'Task' tools are added dynamically by agent-service.ts
+    // based on whether skills/subagents are enabled in settings
+    const defaultTools = ['Read', 'Write', 'Edit', 'Glob', 'Grep', 'Bash', 'WebSearch', 'WebFetch'];
 
     // AUTONOMOUS MODE: Always bypass permissions and allow unrestricted tools
     // Only restrict tools when no MCP servers are configured
diff --git a/apps/server/src/services/agent-service.ts b/apps/server/src/services/agent-service.ts
index 1d543efc..bbc060d1 100644
--- a/apps/server/src/services/agent-service.ts
+++ b/apps/server/src/services/agent-service.ts
@@ -25,6 +25,7 @@ import {
   getMCPServersFromSettings,
   getPromptCustomization,
   getSkillsConfiguration,
+  getSubagentsConfiguration,
   getCustomSubagents,
 } from '../lib/settings-helpers.js';
 
@@ -248,10 +249,16 @@ export class AgentService {
         ? await getSkillsConfiguration(this.settingsService)
         : { enabled: false, sources: [] as Array<'user' | 'project'>, shouldIncludeInTools: false };
 
-      // Get custom subagents from settings (merge global + project-level)
-      const customSubagents = this.settingsService
-        ? await getCustomSubagents(this.settingsService, effectiveWorkDir)
-        : undefined;
+      // Get Subagents configuration from settings
+      const subagentsConfig = this.settingsService
+        ? await getSubagentsConfiguration(this.settingsService)
+        : { enabled: false, sources: [] as Array<'user' | 'project'>, shouldIncludeInTools: false };
+
+      // Get custom subagents from settings (merge global + project-level) only if enabled
+      const customSubagents =
+        this.settingsService && subagentsConfig.enabled
+          ? await getCustomSubagents(this.settingsService, effectiveWorkDir)
+          : undefined;
 
       // Load project context files (CLAUDE.md, CODE_QUALITY.md, etc.)
       const contextResult = await loadContextFiles({
@@ -297,18 +304,34 @@ export class AgentService {
       const settingSources = [...new Set([...sdkSettingSources, ...skillSettingSources])];
 
       // Enhance allowedTools with Skills and Subagents tools
+      // These tools are not in the provider's default set - they're added dynamically based on settings
+      const needsSkillTool = skillsConfig.shouldIncludeInTools;
+      const needsTaskTool =
+        subagentsConfig.shouldIncludeInTools &&
+        customSubagents &&
+        Object.keys(customSubagents).length > 0;
+
+      // Base tools that match the provider's default set
+      const baseTools = ['Read', 'Write', 'Edit', 'Glob', 'Grep', 'Bash', 'WebSearch', 'WebFetch'];
+
       if (allowedTools) {
         allowedTools = [...allowedTools]; // Create a copy to avoid mutating SDK options
         // Add Skill tool if skills are enabled
-        if (skillsConfig.shouldIncludeInTools && !allowedTools.includes('Skill')) {
+        if (needsSkillTool && !allowedTools.includes('Skill')) {
           allowedTools.push('Skill');
         }
         // Add Task tool if custom subagents are configured
-        if (
-          customSubagents &&
-          Object.keys(customSubagents).length > 0 &&
-          !allowedTools.includes('Task')
-        ) {
+        if (needsTaskTool && !allowedTools.includes('Task')) {
+          allowedTools.push('Task');
+        }
+      } else if (needsSkillTool || needsTaskTool) {
+        // If no allowedTools specified but we need to add Skill/Task tools,
+        // build the full list including base tools
+        allowedTools = [...baseTools];
+        if (needsSkillTool) {
+          allowedTools.push('Skill');
+        }
+        if (needsTaskTool) {
           allowedTools.push('Task');
         }
       }
diff --git a/apps/server/tests/unit/providers/claude-provider.test.ts b/apps/server/tests/unit/providers/claude-provider.test.ts
index 3a91652a..40d3b5b7 100644
--- a/apps/server/tests/unit/providers/claude-provider.test.ts
+++ b/apps/server/tests/unit/providers/claude-provider.test.ts
@@ -96,17 +96,9 @@ describe('claude-provider.ts', () => {
       expect(sdk.query).toHaveBeenCalledWith({
         prompt: 'Test',
         options: expect.objectContaining({
-          allowedTools: [
-            'Read',
-            'Write',
-            'Edit',
-            'Glob',
-            'Grep',
-            'Bash',
-            'WebSearch',
-            'WebFetch',
-            'Skill',
-          ],
+          // Note: 'Skill' and 'Task' tools are added dynamically by agent-service.ts
+          // based on settings, not included in base default tools
+          allowedTools: ['Read', 'Write', 'Edit', 'Glob', 'Grep', 'Bash', 'WebSearch', 'WebFetch'],
         }),
       });
     });
diff --git a/apps/ui/src/components/views/settings-view/providers/claude-settings-tab/hooks/use-subagents-settings.ts b/apps/ui/src/components/views/settings-view/providers/claude-settings-tab/hooks/use-subagents-settings.ts
new file mode 100644
index 00000000..ccf7664a
--- /dev/null
+++ b/apps/ui/src/components/views/settings-view/providers/claude-settings-tab/hooks/use-subagents-settings.ts
@@ -0,0 +1,63 @@
+/**
+ * Subagents Settings Hook - Manages Subagents configuration state
+ *
+ * Provides state management for enabling/disabling Subagents and
+ * configuring which sources to load Subagents from (user/project).
+ */
+
+import { useState } from 'react';
+import { useAppStore } from '@/store/app-store';
+import { toast } from 'sonner';
+import { getElectronAPI } from '@/lib/electron';
+
+export function useSubagentsSettings() {
+  const enabled = useAppStore((state) => state.enableSubagents);
+  const sources = useAppStore((state) => state.subagentsSources);
+  const [isLoading, setIsLoading] = useState(false);
+
+  const updateEnabled = async (newEnabled: boolean) => {
+    setIsLoading(true);
+    try {
+      const api = getElectronAPI();
+      if (!api.settings) {
+        throw new Error('Settings API not available');
+      }
+      await api.settings.updateGlobal({ enableSubagents: newEnabled });
+      // Update local store after successful server update
+      useAppStore.setState({ enableSubagents: newEnabled });
+      toast.success(newEnabled ? 'Subagents enabled' : 'Subagents disabled');
+    } catch (error) {
+      toast.error('Failed to update subagents settings');
+      console.error(error);
+    } finally {
+      setIsLoading(false);
+    }
+  };
+
+  const updateSources = async (newSources: Array<'user' | 'project'>) => {
+    setIsLoading(true);
+    try {
+      const api = getElectronAPI();
+      if (!api.settings) {
+        throw new Error('Settings API not available');
+      }
+      await api.settings.updateGlobal({ subagentsSources: newSources });
+      // Update local store after successful server update
+      useAppStore.setState({ subagentsSources: newSources });
+      toast.success('Subagents sources updated');
+    } catch (error) {
+      toast.error('Failed to update subagents sources');
+      console.error(error);
+    } finally {
+      setIsLoading(false);
+    }
+  };
+
+  return {
+    enabled,
+    sources,
+    updateEnabled,
+    updateSources,
+    isLoading,
+  };
+}
diff --git a/apps/ui/src/components/views/settings-view/providers/claude-settings-tab/subagents-section.tsx b/apps/ui/src/components/views/settings-view/providers/claude-settings-tab/subagents-section.tsx
index c6bcd979..08800331 100644
--- a/apps/ui/src/components/views/settings-view/providers/claude-settings-tab/subagents-section.tsx
+++ b/apps/ui/src/components/views/settings-view/providers/claude-settings-tab/subagents-section.tsx
@@ -1,26 +1,62 @@
 /**
- * Subagents Section - UI for viewing filesystem-based agents
+ * Subagents Section - UI for managing Subagents configuration
+ *
+ * Allows users to enable/disable Subagents and select which directories
+ * to load Subagents from (user ~/.claude/agents/ or project .claude/agents/).
  *
  * Displays agents discovered from:
  * - User-level: ~/.claude/agents/
  * - Project-level: .claude/agents/
- *
- * Read-only view - agents are managed by editing .md files directly.
  */
 
 import { Button } from '@/components/ui/button';
+import { Label } from '@/components/ui/label';
+import { Switch } from '@/components/ui/switch';
+import { Checkbox } from '@/components/ui/checkbox';
 import { cn } from '@/lib/utils';
-import { Bot, RefreshCw, Loader2, Users, ExternalLink } from 'lucide-react';
+import {
+  Bot,
+  RefreshCw,
+  Loader2,
+  Users,
+  ExternalLink,
+  Globe,
+  FolderOpen,
+  Sparkles,
+} from 'lucide-react';
 import { useSubagents } from './hooks/use-subagents';
+import { useSubagentsSettings } from './hooks/use-subagents-settings';
 import { SubagentCard } from './subagent-card';
 
 export function SubagentsSection() {
-  const { subagentsWithScope, isLoading, hasProject, refreshFilesystemAgents } = useSubagents();
+  const {
+    subagentsWithScope,
+    isLoading: isLoadingAgents,
+    hasProject,
+    refreshFilesystemAgents,
+  } = useSubagents();
+  const {
+    enabled,
+    sources,
+    updateEnabled,
+    updateSources,
+    isLoading: isLoadingSettings,
+  } = useSubagentsSettings();
+
+  const isLoading = isLoadingAgents || isLoadingSettings;
 
   const handleRefresh = async () => {
     await refreshFilesystemAgents();
   };
 
+  const toggleSource = (source: 'user' | 'project') => {
+    if (sources.includes(source)) {
+      updateSources(sources.filter((s: 'user' | 'project') => s !== source));
+    } else {
+      updateSources([...sources, source]);
+    }
+  };
+
   return (
     <div
       className={cn(
@@ -39,7 +75,7 @@ export function SubagentsSection() {
           <div>
             <h3 className="font-semibold text-base flex items-center gap-2">
               Custom Subagents
-              {subagentsWithScope.length > 0 && (
+              {enabled && subagentsWithScope.length > 0 && (
                 <span className="text-xs font-normal px-2 py-0.5 rounded-full bg-violet-500/20 text-violet-500">
                   {subagentsWithScope.length} agent{subagentsWithScope.length !== 1 ? 's' : ''}
                 </span>
@@ -50,57 +86,169 @@ export function SubagentsSection() {
             </p>
           </div>
         </div>
-        <Button
-          variant="outline"
-          size="sm"
-          onClick={handleRefresh}
+        <Switch
+          id="enable-subagents"
+          checked={enabled}
+          onCheckedChange={updateEnabled}
           disabled={isLoading}
-          title="Refresh agents from disk"
-          className="gap-2"
-        >
-          {isLoading ? (
-            <Loader2 className="h-4 w-4 animate-spin" />
-          ) : (
-            <RefreshCw className="h-4 w-4" />
-          )}
-          <span className="text-xs">Refresh</span>
-        </Button>
+        />
       </div>
 
       {/* Content */}
-      <div className="p-6">
-        {subagentsWithScope.length === 0 ? (
-          <div className="text-center py-8 text-muted-foreground">
-            <Users className="w-12 h-12 mx-auto mb-3 opacity-30" />
-            <p className="text-sm font-medium">No agents found</p>
-            <p className="text-xs mt-2 max-w-sm mx-auto">
-              Create <code className="text-xs bg-muted px-1 rounded">.md</code> files in{' '}
-              <code className="text-xs bg-muted px-1 rounded">~/.claude/agents/</code>
-              {hasProject && (
-                <>
-                  {' or '}
-                  <code className="text-xs bg-muted px-1 rounded">.claude/agents/</code>
-                </>
-              )}
-            </p>
+      <div className="p-6 space-y-4">
+        {/* Sources Selection */}
+        {enabled && (
+          <div className="space-y-3">
+            <Label className="text-xs uppercase tracking-wide text-muted-foreground">
+              Load Subagents from
+            </Label>
+            <div className="grid gap-2">
+              {/* User Subagents Option */}
+              <label
+                htmlFor="subagent-source-user"
+                className={cn(
+                  'flex items-center gap-3 p-3 rounded-xl border cursor-pointer transition-all duration-200',
+                  sources.includes('user')
+                    ? 'border-violet-500/50 bg-violet-500/10'
+                    : 'border-border/50 bg-accent/20 hover:bg-accent/30'
+                )}
+              >
+                <Checkbox
+                  id="subagent-source-user"
+                  checked={sources.includes('user')}
+                  onCheckedChange={() => toggleSource('user')}
+                  disabled={isLoading}
+                  className="data-[state=checked]:bg-violet-500 data-[state=checked]:border-violet-500"
+                />
+                <div className="w-8 h-8 rounded-lg bg-muted/50 flex items-center justify-center shrink-0">
+                  <Globe className="w-4 h-4 text-muted-foreground" />
+                </div>
+                <div className="flex-1 min-w-0">
+                  <span className="text-sm font-medium">User Subagents</span>
+                  <span className="block text-xs text-muted-foreground mt-0.5 truncate">
+                    ~/.claude/agents/ — Available across all projects
+                  </span>
+                </div>
+              </label>
+
+              {/* Project Subagents Option */}
+              <label
+                htmlFor="subagent-source-project"
+                className={cn(
+                  'flex items-center gap-3 p-3 rounded-xl border cursor-pointer transition-all duration-200',
+                  sources.includes('project')
+                    ? 'border-violet-500/50 bg-violet-500/10'
+                    : 'border-border/50 bg-accent/20 hover:bg-accent/30'
+                )}
+              >
+                <Checkbox
+                  id="subagent-source-project"
+                  checked={sources.includes('project')}
+                  onCheckedChange={() => toggleSource('project')}
+                  disabled={isLoading}
+                  className="data-[state=checked]:bg-violet-500 data-[state=checked]:border-violet-500"
+                />
+                <div className="w-8 h-8 rounded-lg bg-muted/50 flex items-center justify-center shrink-0">
+                  <FolderOpen className="w-4 h-4 text-muted-foreground" />
+                </div>
+                <div className="flex-1 min-w-0">
+                  <span className="text-sm font-medium">Project Subagents</span>
+                  <span className="block text-xs text-muted-foreground mt-0.5 truncate">
+                    .claude/agents/ — Version-controlled with project
+                  </span>
+                </div>
+              </label>
+            </div>
+          </div>
+        )}
+
+        {/* Agents List */}
+        {enabled && (
+          <>
+            {/* Refresh Button */}
+            <div className="flex items-center justify-between">
+              <Label className="text-xs uppercase tracking-wide text-muted-foreground">
+                Discovered Agents
+              </Label>
+              <Button
+                variant="ghost"
+                size="sm"
+                onClick={handleRefresh}
+                disabled={isLoading}
+                title="Refresh agents from disk"
+                className="gap-1.5 h-7 px-2 text-xs"
+              >
+                {isLoadingAgents ? (
+                  <Loader2 className="h-3.5 w-3.5 animate-spin" />
+                ) : (
+                  <RefreshCw className="h-3.5 w-3.5" />
+                )}
+                Refresh
+              </Button>
+            </div>
+
+            {subagentsWithScope.length === 0 ? (
+              <div className="text-center py-6 text-muted-foreground border border-dashed border-border/50 rounded-xl">
+                <Users className="w-10 h-10 mx-auto mb-2 opacity-30" />
+                <p className="text-sm font-medium">No agents found</p>
+                <p className="text-xs mt-1 max-w-sm mx-auto">
+                  Create <code className="text-xs bg-muted px-1 rounded">.md</code> files in{' '}
+                  {sources.includes('user') && (
+                    <code className="text-xs bg-muted px-1 rounded">~/.claude/agents/</code>
+                  )}
+                  {sources.includes('user') && sources.includes('project') && ' or '}
+                  {sources.includes('project') && (
+                    <code className="text-xs bg-muted px-1 rounded">.claude/agents/</code>
+                  )}
+                </p>
+              </div>
+            ) : (
+              <div className="space-y-2">
+                {subagentsWithScope.map((agent) => (
+                  <SubagentCard
+                    key={`${agent.type}-${agent.source || agent.scope}-${agent.name}`}
+                    agent={agent}
+                  />
+                ))}
+              </div>
+            )}
+          </>
+        )}
+
+        {/* Help Text */}
+        {enabled && (
+          <div className="rounded-xl border border-border/30 bg-muted/30 p-4 space-y-3">
+            <div className="flex items-start gap-3">
+              <div className="w-6 h-6 rounded-md bg-brand-500/20 flex items-center justify-center shrink-0 mt-0.5">
+                <Sparkles className="w-3.5 h-3.5 text-brand-500" />
+              </div>
+              <div className="text-xs text-muted-foreground space-y-1">
+                <p className="font-medium text-foreground/80">Auto-Discovery</p>
+                <p>
+                  Subagents are automatically discovered when agents start. Define agents as{' '}
+                  <code className="text-xs bg-muted px-1 rounded">AGENT.md</code> files or{' '}
+                  <code className="text-xs bg-muted px-1 rounded">agent-name.md</code> files.
+                </p>
+              </div>
+            </div>
             <a
               href="https://code.claude.com/docs/en/agents"
               target="_blank"
               rel="noopener noreferrer"
-              className="inline-flex items-center gap-1.5 mt-4 text-xs text-brand-500 hover:text-brand-400 transition-colors"
+              className="flex items-center gap-2 text-xs text-brand-500 hover:text-brand-400 transition-colors"
             >
               <ExternalLink className="w-3.5 h-3.5" />
               View Agents documentation
             </a>
           </div>
-        ) : (
-          <div className="space-y-3">
-            {subagentsWithScope.map((agent) => (
-              <SubagentCard
-                key={`${agent.type}-${agent.source || agent.scope}-${agent.name}`}
-                agent={agent}
-              />
-            ))}
+        )}
+
+        {/* Disabled State Empty Message */}
+        {!enabled && (
+          <div className="text-center py-6 text-muted-foreground">
+            <Bot className="w-10 h-10 mx-auto mb-3 opacity-30" />
+            <p className="text-sm">Subagents are disabled</p>
+            <p className="text-xs mt-1">Enable to load custom agent definitions</p>
           </div>
         )}
       </div>
diff --git a/apps/ui/src/hooks/use-settings-migration.ts b/apps/ui/src/hooks/use-settings-migration.ts
index 91374e6e..52ff0b61 100644
--- a/apps/ui/src/hooks/use-settings-migration.ts
+++ b/apps/ui/src/hooks/use-settings-migration.ts
@@ -236,6 +236,8 @@ export async function syncSettingsToServer(): Promise<boolean> {
       mcpServers: state.mcpServers,
       enableSkills: state.enableSkills,
       skillsSources: state.skillsSources,
+      enableSubagents: state.enableSubagents,
+      subagentsSources: state.subagentsSources,
       promptCustomization: state.promptCustomization,
       projects: state.projects,
       trashedProjects: state.trashedProjects,
diff --git a/apps/ui/src/store/app-store.ts b/apps/ui/src/store/app-store.ts
index 6429fadc..6e8853a7 100644
--- a/apps/ui/src/store/app-store.ts
+++ b/apps/ui/src/store/app-store.ts
@@ -516,6 +516,10 @@ export interface AppState {
   enableSkills: boolean; // Enable Skills functionality (loads from .claude/skills/ directories)
   skillsSources: Array<'user' | 'project'>; // Which directories to load Skills from
 
+  // Subagents Configuration
+  enableSubagents: boolean; // Enable Custom Subagents functionality (loads from .claude/agents/ directories)
+  subagentsSources: Array<'user' | 'project'>; // Which directories to load Subagents from
+
   // Prompt Customization
   promptCustomization: PromptCustomization; // Custom prompts for Auto Mode, Agent, Backlog Plan, Enhancement
 
@@ -1028,6 +1032,8 @@ const initialState: AppState = {
   mcpServers: [], // No MCP servers configured by default
   enableSkills: true, // Skills enabled by default
   skillsSources: ['user', 'project'] as Array<'user' | 'project'>, // Load from both sources by default
+  enableSubagents: true, // Subagents enabled by default
+  subagentsSources: ['user', 'project'] as Array<'user' | 'project'>, // Load from both sources by default
   promptCustomization: {}, // Empty by default - all prompts use built-in defaults
   aiProfiles: DEFAULT_AI_PROFILES,
   projectAnalysis: null,
diff --git a/libs/types/src/settings.ts b/libs/types/src/settings.ts
index 4a8814db..c3431f52 100644
--- a/libs/types/src/settings.ts
+++ b/libs/types/src/settings.ts
@@ -504,7 +504,21 @@ export interface GlobalSettings {
 
   // Subagents Configuration
   /**
-   * Custom subagent definitions for specialized task delegation
+   * Enable Custom Subagents functionality (loads from .claude/agents/ directories)
+   * @default true
+   */
+  enableSubagents?: boolean;
+
+  /**
+   * Which directories to load Subagents from
+   * - 'user': ~/.claude/agents/ (personal agents)
+   * - 'project': .claude/agents/ (project-specific agents)
+   * @default ['user', 'project']
+   */
+  subagentsSources?: Array<'user' | 'project'>;
+
+  /**
+   * Custom subagent definitions for specialized task delegation (programmatic)
    * Key: agent name (e.g., 'code-reviewer', 'test-runner')
    * Value: agent configuration
    */
@@ -707,6 +721,10 @@ export const DEFAULT_GLOBAL_SETTINGS: GlobalSettings = {
   enableSandboxMode: false,
   skipSandboxWarning: false,
   mcpServers: [],
+  enableSkills: true,
+  skillsSources: ['user', 'project'],
+  enableSubagents: true,
+  subagentsSources: ['user', 'project'],
 };
 
 /** Default credentials (empty strings - user must provide API keys) */