diff --git a/src/cli/actions/remoteAction.ts b/src/cli/actions/remoteAction.ts
index fe29fc95d..5dd1e0362 100644
--- a/src/cli/actions/remoteAction.ts
+++ b/src/cli/actions/remoteAction.ts
@@ -73,7 +73,7 @@ export const createTempDirectory = async (): Promise<string> => {
 export const cloneRepository = async (
   url: string,
   directory: string,
-  branch?: string,
+  remoteBranch?: string,
   deps = {
     execGitShallowClone,
   },
@@ -82,7 +82,7 @@ export const cloneRepository = async (
   logger.log('');
 
   try {
-    await deps.execGitShallowClone(url, directory, branch);
+    await deps.execGitShallowClone(url, directory, remoteBranch);
   } catch (error) {
     throw new RepomixError(`Failed to clone repository: ${(error as Error).message}`);
   }
diff --git a/src/core/file/gitCommand.ts b/src/core/file/gitCommand.ts
index b8801ee7b..aeeda1279 100644
--- a/src/core/file/gitCommand.ts
+++ b/src/core/file/gitCommand.ts
@@ -1,4 +1,6 @@
 import { exec } from 'node:child_process';
+import fs from 'node:fs/promises';
+import path from 'node:path';
 import { promisify } from 'node:util';
 import { logger } from '../../shared/logger.js';
 
@@ -21,10 +23,46 @@ export const isGitInstalled = async (
 export const execGitShallowClone = async (
   url: string,
   directory: string,
-  branch?: string,
+  remoteBranch?: string,
   deps = {
     execAsync,
   },
 ) => {
-  await deps.execAsync(`git clone --depth 1 ${branch ? `-b ${branch} ` : ''}${url} ${directory}`);
+  if (remoteBranch) {
+    await deps.execAsync(`git -C ${directory} init`);
+    await deps.execAsync(`git -C ${directory} remote add origin ${url}`);
+    try {
+      await deps.execAsync(`git -C ${directory} fetch --depth 1 origin ${remoteBranch}`);
+      await deps.execAsync(`git -C ${directory} checkout FETCH_HEAD`);
+    } catch (err: unknown) {
+      // git fetch --depth 1 origin <short SHA> always throws "couldn't find remote ref" error
+      const isRefNotfoundError =
+        err instanceof Error && err.message.includes(`couldn't find remote ref ${remoteBranch}`);
+
+      if (!isRefNotfoundError) {
+        // Rethrow error as nothing else we can do
+        throw err;
+      }
+
+      // Short SHA detection - matches a hexadecimal string of 4 to 39 characters
+      // If the string matches this regex, it MIGHT be a short SHA
+      // If the string doesn't match, it is DEFINITELY NOT a short SHA
+      const isNotShortSHA = !remoteBranch.match(/^[0-9a-f]{4,39}$/i);
+
+      if (isNotShortSHA) {
+        // Rethrow error as nothing else we can do
+        throw err;
+      }
+
+      // Maybe the error is due to a short SHA, let's try again
+      // Can't use --depth 1 here as we need to fetch the specific commit
+      await deps.execAsync(`git -C ${directory} fetch origin`);
+      await deps.execAsync(`git -C ${directory} checkout ${remoteBranch}`);
+    }
+  } else {
+    await deps.execAsync(`git clone --depth 1 ${url} ${directory}`);
+  }
+
+  // Clean up .git directory
+  await fs.rm(path.join(directory, '.git'), { recursive: true, force: true });
 };
diff --git a/tests/core/file/gitCommand.test.ts b/tests/core/file/gitCommand.test.ts
index 1864390bd..899924af3 100644
--- a/tests/core/file/gitCommand.test.ts
+++ b/tests/core/file/gitCommand.test.ts
@@ -40,39 +40,109 @@ describe('gitCommand', () => {
   });
 
   describe('execGitShallowClone', () => {
-    test('should execute git clone with correct parameters', async () => {
+    test('should execute without branch option if not specified by user', async () => {
       const mockExecAsync = vi.fn().mockResolvedValue({ stdout: '', stderr: '' });
       const url = 'https://github.com/user/repo.git';
       const directory = '/tmp/repo';
-      const branch = 'master';
+      const remoteBranch = undefined;
 
-      await execGitShallowClone(url, directory, branch, { execAsync: mockExecAsync });
+      await execGitShallowClone(url, directory, remoteBranch, { execAsync: mockExecAsync });
 
-      expect(mockExecAsync).toHaveBeenCalledWith(`git clone --depth 1 -b ${branch} ${url} ${directory}`);
+      expect(mockExecAsync).toHaveBeenCalledWith(`git clone --depth 1 ${url} ${directory}`);
     });
-
     test('should throw error when git clone fails', async () => {
       const mockExecAsync = vi.fn().mockRejectedValue(new Error('Authentication failed'));
       const url = 'https://github.com/user/repo.git';
       const directory = '/tmp/repo';
-      const branch = 'master';
+      const remoteBranch = undefined;
 
-      await expect(execGitShallowClone(url, directory, branch, { execAsync: mockExecAsync })).rejects.toThrow(
+      await expect(execGitShallowClone(url, directory, remoteBranch, { execAsync: mockExecAsync })).rejects.toThrow(
         'Authentication failed',
       );
 
-      expect(mockExecAsync).toHaveBeenCalledWith(`git clone --depth 1 -b ${branch} ${url} ${directory}`);
+      expect(mockExecAsync).toHaveBeenCalledWith(`git clone --depth 1 ${url} ${directory}`);
     });
-
-    test('should execute without branch option if not specified by user', async () => {
+    test('should execute commands correctly when branch is specified', async () => {
       const mockExecAsync = vi.fn().mockResolvedValue({ stdout: '', stderr: '' });
+
       const url = 'https://github.com/user/repo.git';
       const directory = '/tmp/repo';
-      const branch = undefined;
+      const remoteBranch = 'main';
 
-      await execGitShallowClone(url, directory, branch, { execAsync: mockExecAsync });
+      await execGitShallowClone(url, directory, remoteBranch, { execAsync: mockExecAsync });
 
-      expect(mockExecAsync).toHaveBeenCalledWith(`git clone --depth 1 ${url} ${directory}`);
+      expect(mockExecAsync).toHaveBeenCalledTimes(4);
+      expect(mockExecAsync).toHaveBeenNthCalledWith(1, `git -C ${directory} init`);
+      expect(mockExecAsync).toHaveBeenNthCalledWith(2, `git -C ${directory} remote add origin ${url}`);
+      expect(mockExecAsync).toHaveBeenNthCalledWith(3, `git -C ${directory} fetch --depth 1 origin ${remoteBranch}`);
+      expect(mockExecAsync).toHaveBeenNthCalledWith(4, `git -C ${directory} checkout FETCH_HEAD`);
+    });
+
+    test('should throw error when git fetch fails', async () => {
+      const mockExecAsync = vi
+        .fn()
+        .mockResolvedValueOnce('Success on first call')
+        .mockResolvedValueOnce('Success on second call')
+        .mockRejectedValueOnce(new Error('Authentication failed'));
+
+      const url = 'https://github.com/user/repo.git';
+      const directory = '/tmp/repo';
+      const remoteBranch = 'b188a6cb39b512a9c6da7235b880af42c78ccd0d';
+
+      await expect(execGitShallowClone(url, directory, remoteBranch, { execAsync: mockExecAsync })).rejects.toThrow(
+        'Authentication failed',
+      );
+      expect(mockExecAsync).toHaveBeenCalledTimes(3);
+      expect(mockExecAsync).toHaveBeenNthCalledWith(1, `git -C ${directory} init`);
+      expect(mockExecAsync).toHaveBeenNthCalledWith(2, `git -C ${directory} remote add origin ${url}`);
+      expect(mockExecAsync).toHaveBeenLastCalledWith(`git -C ${directory} fetch --depth 1 origin ${remoteBranch}`);
+      // The fourth call (e.g., git checkout) won't be made due to the error on the third call
+    });
+
+    test('should handle short SHA correctly', async () => {
+      const url = 'https://github.com/user/repo.git';
+      const directory = '/tmp/repo';
+      const shortSha = 'ce9b621';
+      const mockExecAsync = vi
+        .fn()
+        .mockResolvedValueOnce('Success on first call')
+        .mockResolvedValueOnce('Success on second call')
+        .mockRejectedValueOnce(
+          new Error(
+            `Command failed: git fetch --depth 1 origin ${shortSha}\nfatal: couldn't find remote ref ${shortSha}`,
+          ),
+        );
+
+      await execGitShallowClone(url, directory, shortSha, { execAsync: mockExecAsync });
+
+      expect(mockExecAsync).toHaveBeenCalledTimes(5);
+      expect(mockExecAsync).toHaveBeenNthCalledWith(1, `git -C ${directory} init`);
+      expect(mockExecAsync).toHaveBeenNthCalledWith(2, `git -C ${directory} remote add origin ${url}`);
+      expect(mockExecAsync).toHaveBeenNthCalledWith(3, `git -C ${directory} fetch --depth 1 origin ${shortSha}`);
+      expect(mockExecAsync).toHaveBeenNthCalledWith(4, `git -C ${directory} fetch origin`);
+      expect(mockExecAsync).toHaveBeenLastCalledWith(`git -C ${directory} checkout ${shortSha}`);
+    });
+
+    test("should throw error when remote ref is not found, and it's not due to short SHA", async () => {
+      const url = 'https://github.com/user/repo.git';
+      const directory = '/tmp/repo';
+      const remoteBranch = 'b188a6cb39b512a9c6da7235b880af42c78ccd0d';
+      const errMessage = `Command failed: git fetch --depth 1 origin ${remoteBranch}\nfatal: couldn't find remote ref ${remoteBranch}`;
+
+      const mockExecAsync = vi
+        .fn()
+        .mockResolvedValueOnce('Success on first call')
+        .mockResolvedValueOnce('Success on second call')
+        .mockRejectedValueOnce(new Error(errMessage));
+
+      await expect(execGitShallowClone(url, directory, remoteBranch, { execAsync: mockExecAsync })).rejects.toThrow(
+        errMessage,
+      );
+      expect(mockExecAsync).toHaveBeenCalledTimes(3);
+      expect(mockExecAsync).toHaveBeenNthCalledWith(1, `git -C ${directory} init`);
+      expect(mockExecAsync).toHaveBeenNthCalledWith(2, `git -C ${directory} remote add origin ${url}`);
+      expect(mockExecAsync).toHaveBeenLastCalledWith(`git -C ${directory} fetch --depth 1 origin ${remoteBranch}`);
+      // The fourth call (e.g., git checkout) won't be made due to the error on the third call
     });
   });
 });