diff --git a/packages/core/src/config/config.ts b/packages/core/src/config/config.ts
index bf502090cb..bc89030524 100644
--- a/packages/core/src/config/config.ts
+++ b/packages/core/src/config/config.ts
@@ -1912,7 +1912,9 @@ export class Config {
 
   getTrackerService(): TrackerService {
     if (!this.trackerService) {
-      this.trackerService = new TrackerService(this.targetDir);
+      this.trackerService = new TrackerService(
+        this.storage.getProjectTempTrackerDir(this.sessionId),
+      );
     }
     return this.trackerService;
   }
diff --git a/packages/core/src/services/trackerService.ts b/packages/core/src/services/trackerService.ts
index 6e1fc2abca..8af40c8637 100644
--- a/packages/core/src/services/trackerService.ts
+++ b/packages/core/src/services/trackerService.ts
@@ -12,7 +12,7 @@ import { TrackerTaskSchema, type TrackerTask } from './trackerTypes.js';
 export class TrackerService {
   private readonly tasksDir: string;
 
-  constructor(private readonly trackerDir: string) {
+  constructor(readonly trackerDir: string) {
     this.tasksDir = path.join(this.trackerDir, 'tasks');
   }
 
diff --git a/packages/core/src/tools/trackerTools.test.ts b/packages/core/src/tools/trackerTools.test.ts
index be5bcba5ac..9074caf6d9 100644
--- a/packages/core/src/tools/trackerTools.test.ts
+++ b/packages/core/src/tools/trackerTools.test.ts
@@ -46,9 +46,12 @@ describe('Tracker Tools Integration', () => {
     const result = await tool.buildAndExecute({}, getSignal());
 
     expect(result.llmContent).toContain('Task tracker initialized');
-    const tasksDir = path.join(tempDir, '.tracker', 'tasks');
+    const trackerDir = config.getTrackerService().trackerDir;
+    const tasksDir = path.join(trackerDir, 'tasks');
     const stats = await fs.stat(tasksDir);
     expect(stats.isDirectory()).toBe(true);
+    // Verify it is NOT in the tempDir root (which was the old behavior)
+    expect(trackerDir).not.toBe(path.join(tempDir, '.tracker'));
   });
 
   it('creates and lists tasks', async () => {
diff --git a/packages/core/src/tools/trackerTools.ts b/packages/core/src/tools/trackerTools.ts
index 74efd18f74..ea92fea754 100644
--- a/packages/core/src/tools/trackerTools.ts
+++ b/packages/core/src/tools/trackerTools.ts
@@ -69,8 +69,7 @@ class TrackerInitInvocation extends BaseTrackerInvocation<
   override async execute(_signal: AbortSignal): Promise<ToolResult> {
     await this.service.ensureInitialized();
     return {
-      llmContent:
-        'Task tracker initialized successfully. Storage is ready at .tracker/tasks/',
+      llmContent: `Task tracker initialized successfully. Storage is ready at ${this.service.trackerDir}/tasks/`,
       returnDisplay: 'Tracker initialized.',
     };
   }