diff --git a/apps/server/src/services/auto-loop-coordinator.ts b/apps/server/src/services/auto-loop-coordinator.ts
new file mode 100644
index 00000000..f47cd42b
--- /dev/null
+++ b/apps/server/src/services/auto-loop-coordinator.ts
@@ -0,0 +1,559 @@
+/**
+ * AutoLoopCoordinator - Manages the auto-mode loop lifecycle and failure tracking
+ *
+ * Extracted from AutoModeService to isolate loop control logic (start/stop/pause)
+ * into a focused service for maintainability and testability.
+ *
+ * Key behaviors:
+ * - Loop starts per project/worktree with correct config
+ * - Loop stops when user clicks stop or no work remains
+ * - Failure tracking pauses loop after threshold (agent errors only)
+ * - Multiple project loops run concurrently without interference
+ */
+
+import type { Feature } from '@automaker/types';
+import { createLogger, classifyError } from '@automaker/utils';
+import type { TypedEventBus } from './typed-event-bus.js';
+import type { ConcurrencyManager } from './concurrency-manager.js';
+import type { SettingsService } from './settings-service.js';
+import { DEFAULT_MAX_CONCURRENCY } from '@automaker/types';
+
+const logger = createLogger('AutoLoopCoordinator');
+
+// Constants for consecutive failure tracking
+const CONSECUTIVE_FAILURE_THRESHOLD = 3; // Pause after 3 consecutive failures
+const FAILURE_WINDOW_MS = 60000; // Failures within 1 minute count as consecutive
+
+/**
+ * Configuration for auto-mode loop
+ */
+export interface AutoModeConfig {
+  maxConcurrency: number;
+  useWorktrees: boolean;
+  projectPath: string;
+  branchName: string | null; // null = main worktree
+}
+
+/**
+ * Per-worktree autoloop state for multi-project/worktree support
+ */
+export interface ProjectAutoLoopState {
+  abortController: AbortController;
+  config: AutoModeConfig;
+  isRunning: boolean;
+  consecutiveFailures: { timestamp: number; error: string }[];
+  pausedDueToFailures: boolean;
+  hasEmittedIdleEvent: boolean;
+  branchName: string | null; // null = main worktree
+}
+
+/**
+ * Generate a unique key for worktree-scoped auto loop state
+ * @param projectPath - The project path
+ * @param branchName - The branch name, or null for main worktree
+ */
+export function getWorktreeAutoLoopKey(projectPath: string, branchName: string | null): string {
+  const normalizedBranch = branchName === 'main' ? null : branchName;
+  return `${projectPath}::${normalizedBranch ?? '__main__'}`;
+}
+
+// Callback types for AutoModeService integration
+export type ExecuteFeatureFn = (
+  projectPath: string,
+  featureId: string,
+  useWorktrees: boolean,
+  isAutoMode: boolean
+) => Promise<void>;
+
+export type LoadPendingFeaturesFn = (
+  projectPath: string,
+  branchName: string | null
+) => Promise<Feature[]>;
+
+export type SaveExecutionStateFn = (
+  projectPath: string,
+  branchName: string | null,
+  maxConcurrency: number
+) => Promise<void>;
+
+export type ClearExecutionStateFn = (
+  projectPath: string,
+  branchName: string | null
+) => Promise<void>;
+
+export type ResetStuckFeaturesFn = (projectPath: string) => Promise<void>;
+
+export type IsFeatureFinishedFn = (feature: Feature) => boolean;
+
+/**
+ * AutoLoopCoordinator manages the auto-mode loop lifecycle and failure tracking.
+ * It coordinates feature execution without containing the execution logic itself.
+ */
+export class AutoLoopCoordinator {
+  // Per-project autoloop state (supports multiple concurrent projects)
+  private autoLoopsByProject = new Map<string, ProjectAutoLoopState>();
+
+  constructor(
+    private eventBus: TypedEventBus,
+    private concurrencyManager: ConcurrencyManager,
+    private settingsService: SettingsService | null,
+    private executeFeatureFn: ExecuteFeatureFn,
+    private loadPendingFeaturesFn: LoadPendingFeaturesFn,
+    private saveExecutionStateFn: SaveExecutionStateFn,
+    private clearExecutionStateFn: ClearExecutionStateFn,
+    private resetStuckFeaturesFn: ResetStuckFeaturesFn,
+    private isFeatureFinishedFn: IsFeatureFinishedFn,
+    private isFeatureRunningFn: (featureId: string) => boolean
+  ) {}
+
+  /**
+   * Start the auto mode loop for a specific project/worktree (supports multiple concurrent projects and worktrees)
+   * @param projectPath - The project to start auto mode for
+   * @param branchName - The branch name for worktree scoping, null for main worktree
+   * @param maxConcurrency - Maximum concurrent features (default: DEFAULT_MAX_CONCURRENCY)
+   */
+  async startAutoLoopForProject(
+    projectPath: string,
+    branchName: string | null = null,
+    maxConcurrency?: number
+  ): Promise<number> {
+    const resolvedMaxConcurrency = await this.resolveMaxConcurrency(
+      projectPath,
+      branchName,
+      maxConcurrency
+    );
+
+    // Use worktree-scoped key
+    const worktreeKey = getWorktreeAutoLoopKey(projectPath, branchName);
+
+    // Check if this project/worktree already has an active autoloop
+    const existingState = this.autoLoopsByProject.get(worktreeKey);
+    if (existingState?.isRunning) {
+      const worktreeDesc = branchName ? `worktree ${branchName}` : 'main worktree';
+      throw new Error(
+        `Auto mode is already running for ${worktreeDesc} in project: ${projectPath}`
+      );
+    }
+
+    // Create new project/worktree autoloop state
+    const abortController = new AbortController();
+    const config: AutoModeConfig = {
+      maxConcurrency: resolvedMaxConcurrency,
+      useWorktrees: true,
+      projectPath,
+      branchName,
+    };
+
+    const projectState: ProjectAutoLoopState = {
+      abortController,
+      config,
+      isRunning: true,
+      consecutiveFailures: [],
+      pausedDueToFailures: false,
+      hasEmittedIdleEvent: false,
+      branchName,
+    };
+
+    this.autoLoopsByProject.set(worktreeKey, projectState);
+
+    const worktreeDesc = branchName ? `worktree ${branchName}` : 'main worktree';
+    logger.info(
+      `Starting auto loop for ${worktreeDesc} in project: ${projectPath} with maxConcurrency: ${resolvedMaxConcurrency}`
+    );
+
+    // Reset any features that were stuck in transient states due to previous server crash
+    try {
+      await this.resetStuckFeaturesFn(projectPath);
+    } catch (error) {
+      logger.warn(`[startAutoLoopForProject] Error resetting stuck features:`, error);
+      // Don't fail startup due to reset errors
+    }
+
+    this.eventBus.emitAutoModeEvent('auto_mode_started', {
+      message: `Auto mode started with max ${resolvedMaxConcurrency} concurrent features`,
+      projectPath,
+      branchName,
+      maxConcurrency: resolvedMaxConcurrency,
+    });
+
+    // Save execution state for recovery after restart
+    await this.saveExecutionStateFn(projectPath, branchName, resolvedMaxConcurrency);
+
+    // Run the loop in the background
+    this.runAutoLoopForProject(worktreeKey).catch((error) => {
+      const worktreeDescErr = branchName ? `worktree ${branchName}` : 'main worktree';
+      logger.error(`Loop error for ${worktreeDescErr} in ${projectPath}:`, error);
+      const errorInfo = classifyError(error);
+      this.eventBus.emitAutoModeEvent('auto_mode_error', {
+        error: errorInfo.message,
+        errorType: errorInfo.type,
+        projectPath,
+        branchName,
+      });
+    });
+
+    return resolvedMaxConcurrency;
+  }
+
+  /**
+   * Run the auto loop for a specific project/worktree
+   * @param worktreeKey - The worktree key (projectPath::branchName or projectPath::__main__)
+   */
+  private async runAutoLoopForProject(worktreeKey: string): Promise<void> {
+    const projectState = this.autoLoopsByProject.get(worktreeKey);
+    if (!projectState) {
+      logger.warn(`No project state found for ${worktreeKey}, stopping loop`);
+      return;
+    }
+
+    const { projectPath, branchName } = projectState.config;
+    const worktreeDesc = branchName ? `worktree ${branchName}` : 'main worktree';
+
+    logger.info(
+      `[AutoLoop] Starting loop for ${worktreeDesc} in ${projectPath}, maxConcurrency: ${projectState.config.maxConcurrency}`
+    );
+    let iterationCount = 0;
+
+    while (projectState.isRunning && !projectState.abortController.signal.aborted) {
+      iterationCount++;
+      try {
+        // Count running features for THIS project/worktree only
+        const projectRunningCount = await this.getRunningCountForWorktree(projectPath, branchName);
+
+        // Check if we have capacity for this project/worktree
+        if (projectRunningCount >= projectState.config.maxConcurrency) {
+          logger.debug(
+            `[AutoLoop] At capacity (${projectRunningCount}/${projectState.config.maxConcurrency}), waiting...`
+          );
+          await this.sleep(5000, projectState.abortController.signal);
+          continue;
+        }
+
+        // Load pending features for this project/worktree
+        const pendingFeatures = await this.loadPendingFeaturesFn(projectPath, branchName);
+
+        logger.info(
+          `[AutoLoop] Iteration ${iterationCount}: Found ${pendingFeatures.length} pending features, ${projectRunningCount}/${projectState.config.maxConcurrency} running for ${worktreeDesc}`
+        );
+
+        if (pendingFeatures.length === 0) {
+          // Emit idle event only once when backlog is empty AND no features are running
+          if (projectRunningCount === 0 && !projectState.hasEmittedIdleEvent) {
+            this.eventBus.emitAutoModeEvent('auto_mode_idle', {
+              message: 'No pending features - auto mode idle',
+              projectPath,
+              branchName,
+            });
+            projectState.hasEmittedIdleEvent = true;
+            logger.info(`[AutoLoop] Backlog complete, auto mode now idle for ${worktreeDesc}`);
+          } else if (projectRunningCount > 0) {
+            logger.info(
+              `[AutoLoop] No pending features available, ${projectRunningCount} still running, waiting...`
+            );
+          } else {
+            logger.warn(
+              `[AutoLoop] No pending features found for ${worktreeDesc} (branchName: ${branchName === null ? 'null (main)' : branchName}). Check server logs for filtering details.`
+            );
+          }
+          await this.sleep(10000, projectState.abortController.signal);
+          continue;
+        }
+
+        // Find a feature not currently running and not yet finished
+        const nextFeature = pendingFeatures.find(
+          (f) => !this.isFeatureRunningFn(f.id) && !this.isFeatureFinishedFn(f)
+        );
+
+        if (nextFeature) {
+          logger.info(`[AutoLoop] Starting feature ${nextFeature.id}: ${nextFeature.title}`);
+          // Reset idle event flag since we're doing work again
+          projectState.hasEmittedIdleEvent = false;
+          // Start feature execution in background
+          this.executeFeatureFn(
+            projectPath,
+            nextFeature.id,
+            projectState.config.useWorktrees,
+            true
+          ).catch((error) => {
+            logger.error(`Feature ${nextFeature.id} error:`, error);
+          });
+        } else {
+          logger.debug(`[AutoLoop] All pending features are already running`);
+        }
+
+        await this.sleep(2000, projectState.abortController.signal);
+      } catch (error) {
+        // Check if this is an abort error
+        if (projectState.abortController.signal.aborted) {
+          break;
+        }
+        logger.error(`[AutoLoop] Loop iteration error for ${projectPath}:`, error);
+        await this.sleep(5000, projectState.abortController.signal);
+      }
+    }
+
+    // Mark as not running when loop exits
+    projectState.isRunning = false;
+    logger.info(
+      `[AutoLoop] Loop stopped for project: ${projectPath} after ${iterationCount} iterations`
+    );
+  }
+
+  /**
+   * Stop the auto mode loop for a specific project/worktree
+   * @param projectPath - The project to stop auto mode for
+   * @param branchName - The branch name, or null for main worktree
+   */
+  async stopAutoLoopForProject(
+    projectPath: string,
+    branchName: string | null = null
+  ): Promise<number> {
+    const worktreeKey = getWorktreeAutoLoopKey(projectPath, branchName);
+    const projectState = this.autoLoopsByProject.get(worktreeKey);
+    if (!projectState) {
+      const worktreeDesc = branchName ? `worktree ${branchName}` : 'main worktree';
+      logger.warn(`No auto loop running for ${worktreeDesc} in project: ${projectPath}`);
+      return 0;
+    }
+
+    const wasRunning = projectState.isRunning;
+    projectState.isRunning = false;
+    projectState.abortController.abort();
+
+    // Clear execution state when auto-loop is explicitly stopped
+    await this.clearExecutionStateFn(projectPath, branchName);
+
+    // Emit stop event
+    if (wasRunning) {
+      this.eventBus.emitAutoModeEvent('auto_mode_stopped', {
+        message: 'Auto mode stopped',
+        projectPath,
+        branchName,
+      });
+    }
+
+    // Remove from map
+    this.autoLoopsByProject.delete(worktreeKey);
+
+    return await this.getRunningCountForWorktree(projectPath, branchName);
+  }
+
+  /**
+   * Check if auto mode is running for a specific project/worktree
+   * @param projectPath - The project path
+   * @param branchName - The branch name, or null for main worktree
+   */
+  isAutoLoopRunningForProject(projectPath: string, branchName: string | null = null): boolean {
+    const worktreeKey = getWorktreeAutoLoopKey(projectPath, branchName);
+    const projectState = this.autoLoopsByProject.get(worktreeKey);
+    return projectState?.isRunning ?? false;
+  }
+
+  /**
+   * Get auto loop config for a specific project/worktree
+   * @param projectPath - The project path
+   * @param branchName - The branch name, or null for main worktree
+   */
+  getAutoLoopConfigForProject(
+    projectPath: string,
+    branchName: string | null = null
+  ): AutoModeConfig | null {
+    const worktreeKey = getWorktreeAutoLoopKey(projectPath, branchName);
+    const projectState = this.autoLoopsByProject.get(worktreeKey);
+    return projectState?.config ?? null;
+  }
+
+  /**
+   * Get count of running features for a specific worktree
+   * Delegates to ConcurrencyManager.
+   * @param projectPath - The project path
+   * @param branchName - The branch name, or null for main worktree
+   */
+  async getRunningCountForWorktree(
+    projectPath: string,
+    branchName: string | null
+  ): Promise<number> {
+    return this.concurrencyManager.getRunningCountForWorktree(projectPath, branchName);
+  }
+
+  /**
+   * Track a failure and check if we should pause due to consecutive failures.
+   * @param projectPath - The project to track failure for
+   * @param errorInfo - Error information
+   * @returns true if the loop should be paused
+   */
+  trackFailureAndCheckPauseForProject(
+    projectPath: string,
+    errorInfo: { type: string; message: string }
+  ): boolean {
+    const worktreeKey = getWorktreeAutoLoopKey(projectPath, null);
+    const projectState = this.autoLoopsByProject.get(worktreeKey);
+    if (!projectState) {
+      return false;
+    }
+
+    const now = Date.now();
+
+    // Add this failure
+    projectState.consecutiveFailures.push({ timestamp: now, error: errorInfo.message });
+
+    // Remove old failures outside the window
+    projectState.consecutiveFailures = projectState.consecutiveFailures.filter(
+      (f) => now - f.timestamp < FAILURE_WINDOW_MS
+    );
+
+    // Check if we've hit the threshold
+    if (projectState.consecutiveFailures.length >= CONSECUTIVE_FAILURE_THRESHOLD) {
+      return true; // Should pause
+    }
+
+    // Also immediately pause for known quota/rate limit errors
+    if (errorInfo.type === 'quota_exhausted' || errorInfo.type === 'rate_limit') {
+      return true;
+    }
+
+    return false;
+  }
+
+  /**
+   * Signal that we should pause due to repeated failures or quota exhaustion.
+   * This will pause the auto loop for a specific project.
+   * @param projectPath - The project to pause
+   * @param errorInfo - Error information
+   */
+  signalShouldPauseForProject(
+    projectPath: string,
+    errorInfo: { type: string; message: string }
+  ): void {
+    const worktreeKey = getWorktreeAutoLoopKey(projectPath, null);
+    const projectState = this.autoLoopsByProject.get(worktreeKey);
+    if (!projectState) {
+      return;
+    }
+
+    if (projectState.pausedDueToFailures) {
+      return; // Already paused
+    }
+
+    projectState.pausedDueToFailures = true;
+    const failureCount = projectState.consecutiveFailures.length;
+    logger.info(
+      `Pausing auto loop for ${projectPath} after ${failureCount} consecutive failures. Last error: ${errorInfo.type}`
+    );
+
+    // Emit event to notify UI
+    this.eventBus.emitAutoModeEvent('auto_mode_paused_failures', {
+      message:
+        failureCount >= CONSECUTIVE_FAILURE_THRESHOLD
+          ? `Auto Mode paused: ${failureCount} consecutive failures detected. This may indicate a quota limit or API issue. Please check your usage and try again.`
+          : 'Auto Mode paused: Usage limit or API error detected. Please wait for your quota to reset or check your API configuration.',
+      errorType: errorInfo.type,
+      originalError: errorInfo.message,
+      failureCount,
+      projectPath,
+    });
+
+    // Stop the auto loop for this project
+    this.stopAutoLoopForProject(projectPath);
+  }
+
+  /**
+   * Reset failure tracking for a specific project
+   * @param projectPath - The project to reset failure tracking for
+   */
+  resetFailureTrackingForProject(projectPath: string): void {
+    const worktreeKey = getWorktreeAutoLoopKey(projectPath, null);
+    const projectState = this.autoLoopsByProject.get(worktreeKey);
+    if (projectState) {
+      projectState.consecutiveFailures = [];
+      projectState.pausedDueToFailures = false;
+    }
+  }
+
+  /**
+   * Record a successful feature completion to reset consecutive failure count for a project
+   * @param projectPath - The project to record success for
+   */
+  recordSuccessForProject(projectPath: string): void {
+    const worktreeKey = getWorktreeAutoLoopKey(projectPath, null);
+    const projectState = this.autoLoopsByProject.get(worktreeKey);
+    if (projectState) {
+      projectState.consecutiveFailures = [];
+    }
+  }
+
+  /**
+   * Resolve max concurrency from provided value, settings, or default
+   */
+  private async resolveMaxConcurrency(
+    projectPath: string,
+    branchName: string | null,
+    provided?: number
+  ): Promise<number> {
+    if (typeof provided === 'number' && Number.isFinite(provided)) {
+      return provided;
+    }
+
+    if (!this.settingsService) {
+      return DEFAULT_MAX_CONCURRENCY;
+    }
+
+    try {
+      const settings = await this.settingsService.getGlobalSettings();
+      const globalMax =
+        typeof settings.maxConcurrency === 'number'
+          ? settings.maxConcurrency
+          : DEFAULT_MAX_CONCURRENCY;
+      const projectId = settings.projects?.find((project) => project.path === projectPath)?.id;
+      const autoModeByWorktree = settings.autoModeByWorktree;
+
+      if (projectId && autoModeByWorktree && typeof autoModeByWorktree === 'object') {
+        // Normalize branch name to match UI convention:
+        // - null/undefined -> '__main__' (main worktree)
+        // - 'main' -> '__main__' (matches how UI stores it)
+        // - other branch names -> as-is
+        const normalizedBranch =
+          branchName === null || branchName === undefined || branchName === 'main'
+            ? '__main__'
+            : branchName;
+
+        // Check for worktree-specific setting using worktreeId
+        const worktreeId = `${projectId}::${normalizedBranch}`;
+
+        if (
+          worktreeId in autoModeByWorktree &&
+          typeof autoModeByWorktree[worktreeId]?.maxConcurrency === 'number'
+        ) {
+          logger.debug(
+            `[resolveMaxConcurrency] Using worktree-specific maxConcurrency for ${worktreeId}: ${autoModeByWorktree[worktreeId].maxConcurrency}`
+          );
+          return autoModeByWorktree[worktreeId].maxConcurrency;
+        }
+      }
+
+      return globalMax;
+    } catch (error) {
+      logger.warn(`[resolveMaxConcurrency] Error reading settings, using default:`, error);
+      return DEFAULT_MAX_CONCURRENCY;
+    }
+  }
+
+  /**
+   * Sleep for specified milliseconds, interruptible by abort signal
+   */
+  private sleep(ms: number, signal?: AbortSignal): Promise<void> {
+    return new Promise((resolve, reject) => {
+      if (signal?.aborted) {
+        reject(new Error('Aborted'));
+        return;
+      }
+
+      const timeout = setTimeout(resolve, ms);
+
+      signal?.addEventListener('abort', () => {
+        clearTimeout(timeout);
+        reject(new Error('Aborted'));
+      });
+    });
+  }
+}