diff --git a/packages/cli/src/gemini.tsx b/packages/cli/src/gemini.tsx
index 7bd062ac..11ae1505 100644
--- a/packages/cli/src/gemini.tsx
+++ b/packages/cli/src/gemini.tsx
@@ -22,6 +22,7 @@ import {
 } from './config/settings.js';
 import { themeManager } from './ui/themes/theme-manager.js';
 import { getStartupWarnings } from './utils/startupWarnings.js';
+import { getUserStartupWarnings } from './utils/userStartupWarnings.js';
 import { runNonInteractive } from './nonInteractiveCli.js';
 import { loadExtensions, Extension } from './config/extension.js';
 import { cleanupCheckpoints } from './utils/cleanup.js';
@@ -165,7 +166,10 @@ export async function main() {
     }
   }
   let input = config.getQuestion();
-  const startupWarnings = await getStartupWarnings();
+  const startupWarnings = [
+    ...(await getStartupWarnings()),
+    ...(await getUserStartupWarnings(workspaceRoot)),
+  ];
 
   // Render UI, passing necessary config values. Check that there is no command line question.
   if (process.stdin.isTTY && input?.length === 0) {
diff --git a/packages/cli/src/utils/userStartupWarnings.test.ts b/packages/cli/src/utils/userStartupWarnings.test.ts
new file mode 100644
index 00000000..61053029
--- /dev/null
+++ b/packages/cli/src/utils/userStartupWarnings.test.ts
@@ -0,0 +1,74 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest';
+import { getUserStartupWarnings } from './userStartupWarnings.js';
+import * as os from 'os';
+import fs from 'fs/promises';
+
+vi.mock('os', () => ({
+  default: { homedir: vi.fn() },
+  homedir: vi.fn(),
+}));
+
+vi.mock('fs/promises', () => ({
+  default: { realpath: vi.fn() },
+}));
+
+describe('getUserStartupWarnings', () => {
+  const homeDir = '/home/user';
+
+  beforeEach(() => {
+    vi.mocked(os.homedir).mockReturnValue(homeDir);
+    vi.mocked(fs.realpath).mockImplementation(async (path) => path.toString());
+  });
+
+  afterEach(() => {
+    vi.clearAllMocks();
+  });
+
+  describe('home directory check', () => {
+    it('should return a warning when running in home directory', async () => {
+      vi.mocked(fs.realpath)
+        .mockResolvedValueOnce(homeDir)
+        .mockResolvedValueOnce(homeDir);
+
+      const warnings = await getUserStartupWarnings(homeDir);
+
+      expect(warnings).toContainEqual(
+        expect.stringContaining('home directory'),
+      );
+    });
+
+    it('should not return a warning when running in a project directory', async () => {
+      vi.mocked(fs.realpath)
+        .mockResolvedValueOnce('/some/project/path')
+        .mockResolvedValueOnce(homeDir);
+
+      const warnings = await getUserStartupWarnings('/some/project/path');
+      expect(warnings).not.toContainEqual(
+        expect.stringContaining('home directory'),
+      );
+    });
+
+    it('should handle errors when checking directory', async () => {
+      vi.mocked(fs.realpath)
+        .mockRejectedValueOnce(new Error('FS error'))
+        .mockResolvedValueOnce(homeDir);
+
+      const warnings = await getUserStartupWarnings('/error/path');
+      expect(warnings).toContainEqual(
+        expect.stringContaining('Could not verify'),
+      );
+    });
+  });
+
+  // // Example of how to add a new check:
+  // describe('node version check', () => {
+  //   // Tests for node version check would go here
+  //   // This shows how easy it is to add new test sections
+  // });
+});
diff --git a/packages/cli/src/utils/userStartupWarnings.ts b/packages/cli/src/utils/userStartupWarnings.ts
new file mode 100644
index 00000000..3d76a6e1
--- /dev/null
+++ b/packages/cli/src/utils/userStartupWarnings.ts
@@ -0,0 +1,45 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import fs from 'fs/promises';
+import * as os from 'os';
+
+type WarningCheck = {
+  id: string;
+  check: (workspaceRoot: string) => Promise<string | null>;
+};
+
+// Individual warning checks
+const homeDirectoryCheck: WarningCheck = {
+  id: 'home-directory',
+  check: async (workspaceRoot: string) => {
+    try {
+      const [workspaceRealPath, homeRealPath] = await Promise.all([
+        fs.realpath(workspaceRoot),
+        fs.realpath(os.homedir()),
+      ]);
+
+      if (workspaceRealPath === homeRealPath) {
+        return 'You are running Gemini CLI in your home directory. It is recommended to run in a project-specific directory.';
+      }
+      return null;
+    } catch (_err: unknown) {
+      return 'Could not verify the current directory due to a file system error.';
+    }
+  },
+};
+
+// All warning checks
+const WARNING_CHECKS: readonly WarningCheck[] = [homeDirectoryCheck];
+
+export async function getUserStartupWarnings(
+  workspaceRoot: string,
+): Promise<string[]> {
+  const results = await Promise.all(
+    WARNING_CHECKS.map((check) => check.check(workspaceRoot)),
+  );
+  return results.filter((msg) => msg !== null);
+}