diff --git a/packages/cli/src/config/extension.test.ts b/packages/cli/src/config/extension.test.ts
index c1aa276aadf..b6decd99d5c 100644
--- a/packages/cli/src/config/extension.test.ts
+++ b/packages/cli/src/config/extension.test.ts
@@ -57,7 +57,9 @@ const mockGit = {
   fetch: vi.fn(),
   checkout: vi.fn(),
   listRemote: vi.fn(),
-  revparse: vi.fn(),
+  revparse: vi
+    .fn()
+    .mockResolvedValue('mock-sha-1234567890123456789012345678901234567890'),
   // Not a part of the actual API, but we need to use this to do the correct
   // file system interactions.
   path: vi.fn(),
@@ -170,6 +172,9 @@ describe('extension tests', () => {
 
   beforeEach(() => {
     vi.clearAllMocks();
+    mockGit.revparse.mockResolvedValue(
+      'mock-sha-1234567890123456789012345678901234567890',
+    );
     resetSettingsCacheForTesting();
     keychainData = {};
     mockKeychainStorage = {
diff --git a/packages/cli/src/config/extensions/github.test.ts b/packages/cli/src/config/extensions/github.test.ts
index 830506c0020..f9a508db690 100644
--- a/packages/cli/src/config/extensions/github.test.ts
+++ b/packages/cli/src/config/extensions/github.test.ts
@@ -91,6 +91,9 @@ describe('github.ts', () => {
 
     it('should clone, fetch and checkout a repo', async () => {
       mockGit.getRemotes.mockResolvedValue([{ name: 'origin' }]);
+      mockGit.revparse.mockResolvedValue(
+        'a1b2c3d4e5f6a1b2c3d4e5f6a1b2c3d4e5f6a1b2',
+      );
 
       await cloneFromGit(
         {
@@ -107,7 +110,93 @@ describe('github.ts', () => {
         ['--depth', '1'],
       );
       expect(mockGit.fetch).toHaveBeenCalledWith('origin', 'v1.0.0');
-      expect(mockGit.checkout).toHaveBeenCalledWith('FETCH_HEAD');
+      expect(mockGit.revparse).toHaveBeenCalledWith(['FETCH_HEAD']);
+      expect(mockGit.checkout).toHaveBeenCalledWith(
+        'a1b2c3d4e5f6a1b2c3d4e5f6a1b2c3d4e5f6a1b2',
+      );
+      expect(mockGit.revparse).toHaveBeenCalledWith(['HEAD']);
+    });
+
+    it('should throw error if checked out SHA does not match target SHA', async () => {
+      mockGit.getRemotes.mockResolvedValue([{ name: 'origin' }]);
+      // First call for FETCH_HEAD, second call for HEAD
+      mockGit.revparse
+        .mockResolvedValueOnce('a1b2c3d4e5f6a1b2c3d4e5f6a1b2c3d4e5f6a1b2')
+        .mockResolvedValueOnce('different_malicious_sha');
+
+      await expect(
+        cloneFromGit(
+          {
+            type: 'git',
+            source: 'https://github.com/owner/repo.git',
+            ref: 'v1.0.0',
+          },
+          '/dest',
+        ),
+      ).rejects.toThrow(
+        'Security verification failed: checked out SHA (different_malicious_sha) does not match the target SHA (a1b2c3d4e5f6a1b2c3d4e5f6a1b2c3d4e5f6a1b2)',
+      );
+    });
+
+    it('should throw error if checked out SHA does not match pinned SHA', async () => {
+      mockGit.getRemotes.mockResolvedValue([{ name: 'origin' }]);
+      mockGit.revparse.mockResolvedValue(
+        'a1b2c3d4e5f6a1b2c3d4e5f6a1b2c3d4e5f6a1b2',
+      );
+
+      await expect(
+        cloneFromGit(
+          {
+            type: 'git',
+            source: 'https://github.com/owner/repo.git',
+            ref: 'e9f8d7c6b5a4e9f8d7c6b5a4e9f8d7c6b5a4e9f8', // Pinned SHA
+          },
+          '/dest',
+        ),
+      ).rejects.toThrow(
+        'Security verification failed: checked out SHA (a1b2c3d4e5f6a1b2c3d4e5f6a1b2c3d4e5f6a1b2) does not match the requested pin (e9f8d7c6b5a4e9f8d7c6b5a4e9f8d7c6b5a4e9f8)',
+      );
+    });
+
+    it('should succeed if checked out SHA matches pinned SHA', async () => {
+      mockGit.getRemotes.mockResolvedValue([{ name: 'origin' }]);
+      mockGit.revparse.mockResolvedValue(
+        'a1b2c3d4e5f6a1b2c3d4e5f6a1b2c3d4e5f6a1b2',
+      );
+
+      await cloneFromGit(
+        {
+          type: 'git',
+          source: 'https://github.com/owner/repo.git',
+          ref: 'a1b2c3d4e5f6a1b2c3d4e5f6a1b2c3d4e5f6a1b2', // Pinned SHA matching
+        },
+        '/dest',
+      );
+
+      expect(mockGit.checkout).toHaveBeenCalledWith(
+        'a1b2c3d4e5f6a1b2c3d4e5f6a1b2c3d4e5f6a1b2',
+      );
+    });
+
+    it('should succeed and skip SHA validation if ref is a hex-like branch/tag shorter than 40 characters', async () => {
+      mockGit.getRemotes.mockResolvedValue([{ name: 'origin' }]);
+      mockGit.revparse.mockResolvedValue(
+        'a1b2c3d4e5f6a1b2c3d4e5f6a1b2c3d4e5f6a1b2',
+      );
+
+      await cloneFromGit(
+        {
+          type: 'git',
+          source: 'https://github.com/owner/repo.git',
+          ref: 'deadbeef', // Looks like hex but is shorter than 40 chars (e.g. branch/tag)
+        },
+        '/dest',
+      );
+
+      // Verify that checkout was still called with the resolved target SHA from FETCH_HEAD
+      expect(mockGit.checkout).toHaveBeenCalledWith(
+        'a1b2c3d4e5f6a1b2c3d4e5f6a1b2c3d4e5f6a1b2',
+      );
     });
 
     it('should throw if no remotes found', async () => {
diff --git a/packages/cli/src/config/extensions/github.ts b/packages/cli/src/config/extensions/github.ts
index 06cf344a0d3..ba86e46362a 100644
--- a/packages/cli/src/config/extensions/github.ts
+++ b/packages/cli/src/config/extensions/github.ts
@@ -66,9 +66,35 @@ export async function cloneFromGit(
 
     await git.fetch(remotes[0].name, refToFetch);
 
-    // After fetching, checkout FETCH_HEAD to get the content of the fetched ref.
+    // Resolve FETCH_HEAD to its absolute commit SHA first to bypass any local branch named 'FETCH_HEAD'.
+    const targetSha = (await git.revparse(['FETCH_HEAD'])).trim();
+
+    // After fetching, checkout the resolved SHA to get the content of the fetched ref.
     // This results in a detached HEAD state, which is fine for this purpose.
-    await git.checkout('FETCH_HEAD');
+    await git.checkout(targetSha);
+
+    // Verify checkout integrity
+    const checkedOutSha = (await git.revparse(['HEAD'])).trim();
+    if (checkedOutSha !== targetSha) {
+      throw new Error(
+        `Security verification failed: checked out SHA (${checkedOutSha}) does not match the target SHA (${targetSha}).`,
+      );
+    }
+
+    // If a specific ref was pinned and looks like a SHA, verify that the checked-out commit matches it.
+    if (installMetadata.ref) {
+      const refLower = installMetadata.ref.toLowerCase();
+      // Match only full-length SHA-1 (40 characters) or SHA-256 (64 characters) hashes.
+      // This prevents short hex-only branch/tag names (e.g. ticket numbers or 'deadbeef') from triggering false-positive security errors.
+      const hexRegex = /^(?:[0-9a-f]{40}|[0-9a-f]{64})$/;
+      if (hexRegex.test(refLower)) {
+        if (checkedOutSha.toLowerCase() !== refLower) {
+          throw new Error(
+            `Security verification failed: checked out SHA (${checkedOutSha}) does not match the requested pin (${installMetadata.ref}).`,
+          );
+        }
+      }
+    }
   } catch (error) {
     throw new Error(
       `Failed to clone Git repository from ${installMetadata.source} ${getErrorMessage(error)}`,