diff --git a/packages/cli/src/config/config.test.ts b/packages/cli/src/config/config.test.ts
index 746fc14475..13efe8f517 100644
--- a/packages/cli/src/config/config.test.ts
+++ b/packages/cli/src/config/config.test.ts
@@ -3688,6 +3688,46 @@ describe('loadCliConfig mcpEnabled', () => {
       expect(config.storage.getPlansDir()).not.toContain('ext-plans-dir');
     });
 
+    it('should use tracker directory from active extension when user has not specified one', async () => {
+      process.argv = ['node', 'script.js'];
+      const settings = createTestMergedSettings({
+        experimental: { plan: true },
+      });
+      const argv = await parseArguments(settings);
+
+      vi.spyOn(ExtensionManager.prototype, 'getExtensions').mockReturnValue([
+        {
+          name: 'ext-tracker',
+          isActive: true,
+          tracker: { directory: 'ext-tracker-dir' },
+        } as unknown as GeminiCLIExtension,
+      ]);
+
+      const config = await loadCliConfig(settings, 'test-session', argv);
+      expect(config.storage.getTrackerDir()).toContain('ext-tracker-dir');
+    });
+
+    it('should NOT use tracker directory from active extension when user has specified one', async () => {
+      process.argv = ['node', 'script.js'];
+      const settings = createTestMergedSettings({
+        general: { tracker: { directory: 'user-tracker-dir' } },
+        experimental: { plan: true },
+      });
+      const argv = await parseArguments(settings);
+
+      vi.spyOn(ExtensionManager.prototype, 'getExtensions').mockReturnValue([
+        {
+          name: 'ext-tracker',
+          isActive: true,
+          tracker: { directory: 'ext-tracker-dir' },
+        } as unknown as GeminiCLIExtension,
+      ]);
+
+      const config = await loadCliConfig(settings, 'test-session', argv);
+      expect(config.storage.getTrackerDir()).toContain('user-tracker-dir');
+      expect(config.storage.getTrackerDir()).not.toContain('ext-tracker-dir');
+    });
+
     it('should NOT use plan directory from inactive extension', async () => {
       process.argv = ['node', 'script.js'];
       const settings = createTestMergedSettings({
@@ -3709,6 +3749,27 @@ describe('loadCliConfig mcpEnabled', () => {
       );
     });
 
+    it('should NOT use tracker directory from inactive extension', async () => {
+      process.argv = ['node', 'script.js'];
+      const settings = createTestMergedSettings({
+        experimental: { plan: true },
+      });
+      const argv = await parseArguments(settings);
+
+      vi.spyOn(ExtensionManager.prototype, 'getExtensions').mockReturnValue([
+        {
+          name: 'ext-tracker',
+          isActive: false,
+          tracker: { directory: 'ext-tracker-dir-inactive' },
+        } as unknown as GeminiCLIExtension,
+      ]);
+
+      const config = await loadCliConfig(settings, 'test-session', argv);
+      expect(config.storage.getTrackerDir()).not.toContain(
+        'ext-tracker-dir-inactive',
+      );
+    });
+
     it('should use default path if neither user nor extension settings provide a plan directory', async () => {
       process.argv = ['node', 'script.js'];
       const settings = createTestMergedSettings({
diff --git a/packages/cli/src/config/config.ts b/packages/cli/src/config/config.ts
index 227ad4e8ed..2e797942ba 100755
--- a/packages/cli/src/config/config.ts
+++ b/packages/cli/src/config/config.ts
@@ -570,9 +570,17 @@ export async function loadCliConfig(
   });
   await extensionManager.loadExtensions();
 
-  const extensionPlanSettings = extensionManager
+  const activeExtensions = extensionManager
     .getExtensions()
-    .find((ext) => ext.isActive && ext.plan?.directory)?.plan;
+    .filter((ext) => ext.isActive);
+
+  const extensionPlanSettings = activeExtensions.find(
+    (ext) => !!ext.plan?.directory,
+  )?.plan;
+
+  const extensionTrackerSettings = activeExtensions.find(
+    (ext) => !!ext.tracker?.directory,
+  )?.tracker;
 
   const experimentalJitContext = settings.experimental.jitContext;
 
@@ -931,6 +939,9 @@ export async function loadCliConfig(
     planSettings: settings.general?.plan?.directory
       ? settings.general.plan
       : (extensionPlanSettings ?? settings.general?.plan),
+    trackerSettings: settings.general?.tracker?.directory
+      ? settings.general.tracker
+      : (extensionTrackerSettings ?? settings.general?.tracker),
     enableEventDrivenScheduler: true,
     skillsSupport: settings.skills?.enabled ?? true,
     disabledSkills: settings.skills?.disabled,
diff --git a/packages/cli/src/config/extension-manager.ts b/packages/cli/src/config/extension-manager.ts
index 90413fd78a..fd8d72399f 100644
--- a/packages/cli/src/config/extension-manager.ts
+++ b/packages/cli/src/config/extension-manager.ts
@@ -1050,6 +1050,7 @@ Would you like to attempt to install via "git clone" instead?`,
         rules,
         checkers,
         plan: config.plan,
+        tracker: config.tracker,
       };
     } catch (e) {
       const extName = path.basename(extensionDir);
diff --git a/packages/cli/src/config/extension.ts b/packages/cli/src/config/extension.ts
index a29479b4d8..7344fd8546 100644
--- a/packages/cli/src/config/extension.ts
+++ b/packages/cli/src/config/extension.ts
@@ -42,6 +42,15 @@ export interface ExtensionConfig {
      */
     directory?: string;
   };
+  /**
+   * Task tracking configuration contributed by this extension.
+   */
+  tracker?: {
+    /**
+     * The directory where task tracking data is stored.
+     */
+    directory?: string;
+  };
   /**
    * Used to migrate an extension to a new repository source.
    */
diff --git a/packages/cli/src/config/settingsSchema.test.ts b/packages/cli/src/config/settingsSchema.test.ts
index 37ddf87642..69b51eae94 100644
--- a/packages/cli/src/config/settingsSchema.test.ts
+++ b/packages/cli/src/config/settingsSchema.test.ts
@@ -125,6 +125,16 @@ describe('SettingsSchema', () => {
       ).toBe('string');
     });
 
+    it('should have tracker nested properties', () => {
+      expect(
+        getSettingsSchema().general?.properties?.tracker?.properties?.directory,
+      ).toBeDefined();
+      expect(
+        getSettingsSchema().general?.properties?.tracker?.properties?.directory
+          .type,
+      ).toBe('string');
+    });
+
     it('should have fileFiltering nested properties', () => {
       expect(
         getSettingsSchema().context.properties.fileFiltering.properties
diff --git a/packages/cli/src/config/settingsSchema.ts b/packages/cli/src/config/settingsSchema.ts
index 97d35953bb..b6665c3fef 100644
--- a/packages/cli/src/config/settingsSchema.ts
+++ b/packages/cli/src/config/settingsSchema.ts
@@ -315,6 +315,27 @@ const SETTINGS_SCHEMA = {
           },
         },
       },
+      tracker: {
+        type: 'object',
+        label: 'Task Tracker',
+        category: 'General',
+        requiresRestart: true,
+        default: {},
+        description: 'Task tracking features configuration.',
+        showInDialog: false,
+        properties: {
+          directory: {
+            type: 'string',
+            label: 'Tracker Directory',
+            category: 'General',
+            requiresRestart: true,
+            default: undefined as string | undefined,
+            description:
+              'The directory where task tracking data is stored. If not specified, defaults to the system temporary directory.',
+            showInDialog: true,
+          },
+        },
+      },
       retryFetchErrors: {
         type: 'boolean',
         label: 'Retry Fetch Errors',
diff --git a/packages/core/src/config/config.ts b/packages/core/src/config/config.ts
index 89b3af04bc..6995ab915c 100644
--- a/packages/core/src/config/config.ts
+++ b/packages/core/src/config/config.ts
@@ -184,6 +184,10 @@ export interface PlanSettings {
   modelRouting?: boolean;
 }
 
+export interface TrackerSettings {
+  directory?: string;
+}
+
 export interface TelemetrySettings {
   enabled?: boolean;
   target?: TelemetryTarget;
@@ -375,6 +379,10 @@ export interface GeminiCLIExtension {
      */
     directory?: string;
   };
+  /**
+   * Task tracking configuration contributed by this extension.
+   */
+  tracker?: TrackerSettings;
   /**
    * Used to migrate an extension to a new repository source.
    */
@@ -657,6 +665,7 @@ export interface ConfigParameters {
   plan?: boolean;
   tracker?: boolean;
   planSettings?: PlanSettings;
+  trackerSettings?: TrackerSettings;
   worktreeSettings?: WorktreeSettings;
   modelSteering?: boolean;
   onModelChange?: (model: string) => void;
@@ -1136,6 +1145,7 @@ export class Config implements McpContext, AgentLoopContext {
     this.enableExtensionReloading = params.enableExtensionReloading ?? false;
     this.storage = new Storage(this.targetDir, this._sessionId);
     this.storage.setCustomPlansDir(params.planSettings?.directory);
+    this.storage.setCustomTrackerDir(params.trackerSettings?.directory);
 
     this.fakeResponses = params.fakeResponses;
     this.recordResponses = params.recordResponses;
@@ -2541,9 +2551,7 @@ export class Config implements McpContext, AgentLoopContext {
 
   getTrackerService(): TrackerService {
     if (!this.trackerService) {
-      this.trackerService = new TrackerService(
-        this.storage.getProjectTempTrackerDir(),
-      );
+      this.trackerService = new TrackerService(this.storage.getTrackerDir());
     }
     return this.trackerService;
   }
diff --git a/packages/core/src/config/storage.test.ts b/packages/core/src/config/storage.test.ts
index ea8fce6da3..d49ecb6477 100644
--- a/packages/core/src/config/storage.test.ts
+++ b/packages/core/src/config/storage.test.ts
@@ -371,6 +371,78 @@ describe('Storage – additional helpers', () => {
       });
     });
   });
+
+  describe('getTrackerDir', () => {
+    interface TestCase {
+      name: string;
+      customDir: string | undefined;
+      expected: string | (() => string);
+      expectedError?: string;
+      setup?: () => () => void;
+    }
+
+    const testCases: TestCase[] = [
+      {
+        name: 'custom relative path',
+        customDir: '.gemini/tracker',
+        expected: path.resolve(projectRoot, '.gemini/tracker'),
+      },
+      {
+        name: 'custom absolute path outside throws',
+        customDir: '/absolute/path/to/tracker',
+        expected: '',
+        expectedError: `Custom tracker directory '/absolute/path/to/tracker' resolves to '/absolute/path/to/tracker', which is outside the project root '${resolveToRealPath(projectRoot)}'.`,
+      },
+      {
+        name: 'absolute path that happens to be inside project root',
+        customDir: path.join(projectRoot, '.gemini/tracker'),
+        expected: path.join(projectRoot, '.gemini/tracker'),
+      },
+      {
+        name: 'relative path that stays within project root',
+        customDir: 'subdir/../tracker',
+        expected: path.resolve(projectRoot, 'tracker'),
+      },
+      {
+        name: 'dot path',
+        customDir: '.',
+        expected: projectRoot,
+      },
+      {
+        name: 'default behavior when customDir is undefined',
+        customDir: undefined,
+        expected: () => storage.getProjectTempTrackerDir(),
+      },
+      {
+        name: 'escaping relative path throws',
+        customDir: '../escaped-tracker',
+        expected: '',
+        expectedError: `Custom tracker directory '../escaped-tracker' resolves to '${resolveToRealPath(path.resolve(projectRoot, '../escaped-tracker'))}', which is outside the project root '${resolveToRealPath(projectRoot)}'.`,
+      },
+    ];
+
+    testCases.forEach(({ name, customDir, expected, expectedError, setup }) => {
+      it(`should handle ${name}`, async () => {
+        const cleanup = setup?.();
+        try {
+          if (name.includes('default behavior')) {
+            await storage.initialize();
+          }
+
+          storage.setCustomTrackerDir(customDir);
+          if (expectedError) {
+            expect(() => storage.getTrackerDir()).toThrow(expectedError);
+          } else {
+            const expectedValue =
+              typeof expected === 'function' ? expected() : expected;
+            expect(storage.getTrackerDir()).toBe(expectedValue);
+          }
+        } finally {
+          cleanup?.();
+        }
+      });
+    });
+  });
 });
 
 describe('Storage - System Paths', () => {
diff --git a/packages/core/src/config/storage.ts b/packages/core/src/config/storage.ts
index 38654346fa..2857602086 100644
--- a/packages/core/src/config/storage.ts
+++ b/packages/core/src/config/storage.ts
@@ -32,6 +32,7 @@ export class Storage {
   private projectIdentifier: string | undefined;
   private initPromise: Promise<void> | undefined;
   private customPlansDir: string | undefined;
+  private customTrackerDir: string | undefined;
 
   constructor(targetDir: string, sessionId?: string) {
     this.targetDir = targetDir;
@@ -42,6 +43,10 @@ export class Storage {
     this.customPlansDir = dir;
   }
 
+  setCustomTrackerDir(dir: string | undefined): void {
+    this.customTrackerDir = dir;
+  }
+
   static getGlobalGeminiDir(): string {
     const homeDir = homedir();
     if (!homeDir) {
@@ -328,6 +333,26 @@ export class Storage {
     return this.getProjectTempPlansDir();
   }
 
+  getTrackerDir(): string {
+    if (this.customTrackerDir) {
+      const resolvedPath = path.resolve(
+        this.getProjectRoot(),
+        this.customTrackerDir,
+      );
+      const realProjectRoot = resolveToRealPath(this.getProjectRoot());
+      const realResolvedPath = resolveToRealPath(resolvedPath);
+
+      if (!isSubpath(realProjectRoot, realResolvedPath)) {
+        throw new Error(
+          `Custom tracker directory '${this.customTrackerDir}' resolves to '${realResolvedPath}', which is outside the project root '${realProjectRoot}'.`,
+        );
+      }
+
+      return resolvedPath;
+    }
+    return this.getProjectTempTrackerDir();
+  }
+
   getProjectTempTasksDir(): string {
     if (this.sessionId) {
       return path.join(this.getProjectTempDir(), this.sessionId, 'tasks');