diff --git a/packages/cli/src/utils/userStartupWarnings.test.ts b/packages/cli/src/utils/userStartupWarnings.test.ts
index d255dc1d3a7..ed49c7104ad 100644
--- a/packages/cli/src/utils/userStartupWarnings.test.ts
+++ b/packages/cli/src/utils/userStartupWarnings.test.ts
@@ -29,10 +29,9 @@ vi.mock('os', async (importOriginal) => {
 
 vi.mock('@google/gemini-cli-core', async (importOriginal) => {
   const actual =
-    await importOriginal<typeof import('@google/gemini-cli-core')>();
+    await importOriginal<typeof import('@google-gemini-cli-core')>();
   return {
     ...actual,
-    homedir: () => os.homedir(),
     getCompatibilityWarnings: vi.fn().mockReturnValue([]),
     isHeadlessMode: vi.fn().mockReturnValue(false),
     WarningPriority: {
@@ -108,6 +107,60 @@ describe('getUserStartupWarnings', () => {
       const warnings = await getUserStartupWarnings({}, homeDir);
       expect(warnings.find((w) => w.id === 'home-directory')).toBeUndefined();
     });
+
+    it('should not return a warning when running in a subdirectory of home', async () => {
+      const subDir = path.join(homeDir, 'projects', 'my-app');
+      await fs.mkdir(subDir, { recursive: true });
+      const warnings = await getUserStartupWarnings({}, subDir);
+      expect(warnings.find((w) => w.id === 'home-directory')).toBeUndefined();
+    });
+
+    it('should not return a warning when home directory is a symlink and running in a subdirectory', async () => {
+      const realHome = path.join(testRootDir, 'real-home');
+      await fs.mkdir(realHome, { recursive: true });
+      const symlinkedHome = path.join(testRootDir, 'symlinked-home');
+      await fs.symlink(realHome, symlinkedHome);
+      vi.mocked(os.homedir).mockReturnValue(symlinkedHome);
+
+      const subDir = path.join(symlinkedHome, 'projects');
+      await fs.mkdir(subDir, { recursive: true });
+      const warnings = await getUserStartupWarnings({}, subDir);
+      expect(warnings.find((w) => w.id === 'home-directory')).toBeUndefined();
+    });
+
+    it('should return a warning when home directory is a symlink and running in it', async () => {
+      const realHome = path.join(testRootDir, 'real-home2');
+      await fs.mkdir(realHome, { recursive: true });
+      const symlinkedHome = path.join(testRootDir, 'symlinked-home2');
+      await fs.symlink(realHome, symlinkedHome);
+      vi.mocked(os.homedir).mockReturnValue(symlinkedHome);
+
+      const warnings = await getUserStartupWarnings({}, symlinkedHome);
+      expect(warnings).toContainEqual(
+        expect.objectContaining({
+          id: 'home-directory',
+          message: expect.stringContaining(
+            'Warning you are running Gemini CLI in your home directory',
+          ),
+          priority: WarningPriority.Low,
+        }),
+      );
+    });
+
+    it('should not return a warning when GEMINI_CLI_HOME differs from os.homedir', async () => {
+      const projectDir = path.join(testRootDir, 'project');
+      await fs.mkdir(projectDir, { recursive: true });
+      vi.stubEnv('GEMINI_CLI_HOME', projectDir);
+
+      const warnings = await getUserStartupWarnings({}, projectDir);
+      expect(warnings.find((w) => w.id === 'home-directory')).toBeUndefined();
+    });
+  });
+
+  afterEach(async () => {
+    await fs.rm(testRootDir, { recursive: true, force: true });
+    vi.unstubAllEnvs();
+    vi.restoreAllMocks();
   });
 
   describe('root directory check', () => {
diff --git a/packages/cli/src/utils/userStartupWarnings.ts b/packages/cli/src/utils/userStartupWarnings.ts
index 549b62f859d..75530b264fa 100644
--- a/packages/cli/src/utils/userStartupWarnings.ts
+++ b/packages/cli/src/utils/userStartupWarnings.ts
@@ -5,10 +5,10 @@
  */
 
 import fs from 'node:fs/promises';
+import { homedir as osHomedir } from 'node:os';
 import path from 'node:path';
 import process from 'node:process';
 import {
-  homedir,
   getCompatibilityWarnings,
   WarningPriority,
   type StartupWarning,
@@ -39,7 +39,7 @@ const homeDirectoryCheck: WarningCheck = {
     try {
       const [workspaceRealPath, homeRealPath] = await Promise.all([
         fs.realpath(workspaceRoot),
-        fs.realpath(homedir()),
+        fs.realpath(osHomedir()),
       ]);
 
       if (workspaceRealPath === homeRealPath) {