diff --git a/apps/app/src/components/views/board-view/hooks/use-board-actions.ts b/apps/app/src/components/views/board-view/hooks/use-board-actions.ts
index 7cf3c71d..787b2ed2 100644
--- a/apps/app/src/components/views/board-view/hooks/use-board-actions.ts
+++ b/apps/app/src/components/views/board-view/hooks/use-board-actions.ts
@@ -342,7 +342,8 @@ export function useBoardActions({
 
         const result = await api.autoMode.resumeFeature(
           currentProject.path,
-          feature.id
+          feature.id,
+          useWorktrees
         );
 
         if (result.success) {
@@ -356,7 +357,7 @@ export function useBoardActions({
         await loadFeatures();
       }
     },
-    [currentProject, loadFeatures]
+    [currentProject, loadFeatures, useWorktrees]
   );
 
   const handleManualVerify = useCallback(
diff --git a/apps/app/src/lib/electron.ts b/apps/app/src/lib/electron.ts
index 13606ee3..4787462e 100644
--- a/apps/app/src/lib/electron.ts
+++ b/apps/app/src/lib/electron.ts
@@ -233,7 +233,8 @@ export interface AutoModeAPI {
   ) => Promise<{ success: boolean; passes?: boolean; error?: string }>;
   resumeFeature: (
     projectPath: string,
-    featureId: string
+    featureId: string,
+    useWorktrees?: boolean
   ) => Promise<{ success: boolean; passes?: boolean; error?: string }>;
   contextExists: (
     projectPath: string,
@@ -1464,7 +1465,7 @@ function createMockAutoModeAPI(): AutoModeAPI {
       return { success: true, passes: true };
     },
 
-    resumeFeature: async (projectPath: string, featureId: string) => {
+    resumeFeature: async (projectPath: string, featureId: string, useWorktrees?: boolean) => {
       if (mockRunningFeatures.has(featureId)) {
         return {
           success: false,
diff --git a/apps/app/src/lib/http-api-client.ts b/apps/app/src/lib/http-api-client.ts
index 8dbc5512..d43d8322 100644
--- a/apps/app/src/lib/http-api-client.ts
+++ b/apps/app/src/lib/http-api-client.ts
@@ -536,8 +536,8 @@ export class HttpApiClient implements ElectronAPI {
       }),
     verifyFeature: (projectPath: string, featureId: string) =>
       this.post("/api/auto-mode/verify-feature", { projectPath, featureId }),
-    resumeFeature: (projectPath: string, featureId: string) =>
-      this.post("/api/auto-mode/resume-feature", { projectPath, featureId }),
+    resumeFeature: (projectPath: string, featureId: string, useWorktrees?: boolean) =>
+      this.post("/api/auto-mode/resume-feature", { projectPath, featureId, useWorktrees }),
     contextExists: (projectPath: string, featureId: string) =>
       this.post("/api/auto-mode/context-exists", { projectPath, featureId }),
     analyzeProject: (projectPath: string) =>
diff --git a/apps/app/src/types/electron.d.ts b/apps/app/src/types/electron.d.ts
index 3d45d4c4..aa244fbe 100644
--- a/apps/app/src/types/electron.d.ts
+++ b/apps/app/src/types/electron.d.ts
@@ -359,7 +359,8 @@ export interface AutoModeAPI {
 
   resumeFeature: (
     projectPath: string,
-    featureId: string
+    featureId: string,
+    useWorktrees?: boolean
   ) => Promise<{
     success: boolean;
     passes?: boolean;
diff --git a/apps/server/src/routes/auto-mode/routes/resume-feature.ts b/apps/server/src/routes/auto-mode/routes/resume-feature.ts
index 73007d91..94f5b056 100644
--- a/apps/server/src/routes/auto-mode/routes/resume-feature.ts
+++ b/apps/server/src/routes/auto-mode/routes/resume-feature.ts
@@ -29,8 +29,9 @@ export function createResumeFeatureHandler(autoModeService: AutoModeService) {
       }
 
       // Start resume in background
+      // Default to false - worktrees should only be used when explicitly enabled
       autoModeService
-        .resumeFeature(projectPath, featureId, useWorktrees ?? true)
+        .resumeFeature(projectPath, featureId, useWorktrees ?? false)
         .catch((error) => {
           logger.error(`[AutoMode] Resume feature ${featureId} error:`, error);
         });
diff --git a/apps/server/src/routes/auto-mode/routes/run-feature.ts b/apps/server/src/routes/auto-mode/routes/run-feature.ts
index 056acbfd..da2f1f6c 100644
--- a/apps/server/src/routes/auto-mode/routes/run-feature.ts
+++ b/apps/server/src/routes/auto-mode/routes/run-feature.ts
@@ -31,8 +31,9 @@ export function createRunFeatureHandler(autoModeService: AutoModeService) {
 
       // Start execution in background
       // If worktreePath is provided, use it directly; otherwise let the service decide
+      // Default to false - worktrees should only be used when explicitly enabled
       autoModeService
-        .executeFeature(projectPath, featureId, useWorktrees ?? true, false, worktreePath)
+        .executeFeature(projectPath, featureId, useWorktrees ?? false, false, worktreePath)
         .catch((error) => {
           logger.error(`[AutoMode] Feature ${featureId} error:`, error);
         });
diff --git a/apps/server/src/services/auto-mode-service.ts b/apps/server/src/services/auto-mode-service.ts
index 24212514..7d779da8 100644
--- a/apps/server/src/services/auto-mode-service.ts
+++ b/apps/server/src/services/auto-mode-service.ts
@@ -193,7 +193,7 @@ export class AutoModeService {
   async executeFeature(
     projectPath: string,
     featureId: string,
-    useWorktrees = true,
+    useWorktrees = false,
     isAutoMode = false,
     providedWorktreePath?: string
   ): Promise<void> {
@@ -352,7 +352,7 @@ export class AutoModeService {
   async resumeFeature(
     projectPath: string,
     featureId: string,
-    useWorktrees = true
+    useWorktrees = false
   ): Promise<void> {
     // Check if context exists in .automaker directory
     const featureDir = getFeatureDir(projectPath, featureId);