diff --git a/packages/rstack/src/cli/commandHelp.ts b/packages/rstack/src/cli/commandHelp.ts
index 2b6398e5..a844a1b4 100644
--- a/packages/rstack/src/cli/commandHelp.ts
+++ b/packages/rstack/src/cli/commandHelp.ts
@@ -498,6 +498,7 @@ const HELP_DEFINITIONS = {
       {
         title: 'Options',
         items: [
+          ['-f, --force', 'Install despite an existing Git hooks setup'],
           [
             '--hooks-dir <path>',
             'Specify hooks directory relative to the Git repository root',
diff --git a/packages/rstack/src/setup/index.ts b/packages/rstack/src/setup/index.ts
index ef597323..5b37d61d 100644
--- a/packages/rstack/src/setup/index.ts
+++ b/packages/rstack/src/setup/index.ts
@@ -7,6 +7,7 @@ export const runSetupCLI = async (args: string[]): Promise<void> => {
   const { values } = parseArgs({
     args,
     options: {
+      force: { type: 'boolean', short: 'f' },
       help: { type: 'boolean', short: 'h' },
       'hooks-dir': { type: 'string', multiple: true },
     },
@@ -28,15 +29,47 @@ export const runSetupCLI = async (args: string[]): Promise<void> => {
     return;
   }
 
-  const result = installHooks({ hooksDir });
+  const result = installHooks({ force: values.force, hooksDir });
 
-  if (result.status === 'installed' || result.status === 'unchanged') {
+  if (result.status === 'installed') {
+    // Warn when `--force` preserves an existing hooks setup but makes it inactive.
+    if (result.inactiveHooks) {
+      const { hooks, path, restore } = result.inactiveHooks;
+      const hooksMessage = hooks.length
+        ? `: ${color.yellow(hooks.join(', '))}`
+        : '';
+      logger.warn(
+        `The previous Git hooks path "${color.yellow(path)}" is now inactive${hooksMessage}.`,
+      );
+
+      if (restore === 'unset') {
+        logger.info(
+          `The existing files were preserved and will become active again if ${color.yellow('core.hooksPath')} is unset.`,
+        );
+      } else {
+        logger.info(
+          `The existing files were preserved. Set ${color.yellow('core.hooksPath')} back to this path to use them again.`,
+        );
+      }
+    }
+    return;
+  }
+
+  if (result.status === 'unchanged') {
     return;
   }
 
   if (result.status === 'skipped') {
     if (result.message) {
       logger.warn(`Git hooks setup skipped: ${color.yellow(result.message)}.`);
+      if (
+        result.reason === 'existing-git-hooks' ||
+        result.reason === 'hooks-path-conflict'
+      ) {
+        logger.info(
+          `To continue, run ${color.yellow('rs setup --force')}. Existing hook files will be preserved but become inactive.`,
+        );
+      }
       return;
     }
 
diff --git a/packages/rstack/src/setup/install.ts b/packages/rstack/src/setup/install.ts
index eae7c186..92a65842 100644
--- a/packages/rstack/src/setup/install.ts
+++ b/packages/rstack/src/setup/install.ts
@@ -17,9 +17,16 @@ const gitignore = '*\n';
 
 type InstallHooksOptions = {
   cwd?: string;
+  force?: boolean;
   hooksDir?: string;
 };
 
+type InactiveHooks = {
+  hooks: string[];
+  path: string;
+  restore: 'configure' | 'unset';
+};
+
 type FailedInstallResult = {
   status: 'failed';
   reason: string;
@@ -33,7 +40,7 @@ type SkippedInstallResult = {
 };
 
 type InstallResult =
-  | { status: 'installed'; hooksPath: string }
+  | { status: 'installed'; hooksPath: string; inactiveHooks?: InactiveHooks }
   | { status: 'unchanged'; hooksPath: string }
   | SkippedInstallResult
   | FailedInstallResult;
@@ -252,6 +259,7 @@ const findExistingHooks = (directory: string): string[] =>
 
 export const installHooks = ({
   cwd = process.cwd(),
+  force = false,
   hooksDir = defaultHooksDir,
 }: InstallHooksOptions = {}): InstallResult => {
   if (process.env.RSTACK_HOOKS === '0') {
@@ -282,16 +290,24 @@ export const installHooks = ({
     effectiveHooksDirectory,
     defaultHooksDirectory,
   );
+  let inactiveHooks: InactiveHooks | undefined;
 
   if (!hooksPathMatches && !usesDefaultHooks) {
     const activeOwner = readOwner(effectiveHooksDirectory);
     if (!activeOwner) {
-      return skip(
-        'hooks-path-conflict',
-        `Git hooks are already configured at "${displayPath(gitRoot, effectiveHooksDirectory)}"`,
-      );
-    }
-    if (activeOwner !== projectPath) {
+      if (!force) {
+        return skip(
+          'hooks-path-conflict',
+          `Git hooks are already configured at "${displayPath(gitRoot, effectiveHooksDirectory)}"`,
+        );
+      }
+
+      inactiveHooks = {
+        hooks: findExistingHooks(effectiveHooksDirectory),
+        path: displayPath(gitRoot, effectiveHooksDirectory),
+        restore: 'configure',
+      };
+    } else if (activeOwner !== projectPath) {
       return ownerConflict(activeOwner);
     }
   }
@@ -299,10 +315,18 @@ export const installHooks = ({
   if (usesDefaultHooks) {
     const existingHooks = findExistingHooks(defaultHooksDirectory);
     if (existingHooks.length > 0) {
-      return skip(
-        'existing-git-hooks',
-        `existing Git hooks were found: ${existingHooks.join(', ')}`,
-      );
+      if (!force) {
+        return skip(
+          'existing-git-hooks',
+          `existing Git hooks were found: ${existingHooks.join(', ')}`,
+        );
+      }
+
+      inactiveHooks = {
+        hooks: existingHooks,
+        path: displayPath(gitRoot, defaultHooksDirectory),
+        restore: 'unset',
+      };
     }
   }
 
@@ -360,5 +384,9 @@ export const installHooks = ({
     );
   }
 
-  return { status: 'installed', hooksPath };
+  return {
+    status: 'installed',
+    hooksPath,
+    ...(inactiveHooks ? { inactiveHooks } : {}),
+  };
 };
diff --git a/packages/rstack/tests/cli/setup/__snapshots__/index.test.ts.snap b/packages/rstack/tests/cli/setup/__snapshots__/index.test.ts.snap
index d238e172..71351935 100644
--- a/packages/rstack/tests/cli/setup/__snapshots__/index.test.ts.snap
+++ b/packages/rstack/tests/cli/setup/__snapshots__/index.test.ts.snap
@@ -9,6 +9,7 @@ Usage:
 Install Git hooks in the current repository
 
 Options:
+  -f, --force         Install despite an existing Git hooks setup
   --hooks-dir <path>  Specify hooks directory relative to the Git repository root
   -h, --help          Display this help message
 "
diff --git a/packages/rstack/tests/cli/setup/index.test.ts b/packages/rstack/tests/cli/setup/index.test.ts
index 0780fd4a..93bda958 100644
--- a/packages/rstack/tests/cli/setup/index.test.ts
+++ b/packages/rstack/tests/cli/setup/index.test.ts
@@ -1,5 +1,6 @@
 import { spawnSync } from 'node:child_process';
 import {
+  chmodSync,
   existsSync,
   mkdirSync,
   mkdtempSync,
@@ -34,6 +35,16 @@ const runSetup = (args: string[], runCwd: string = cwd) =>
     env,
   });
 
+const runSetupSuccessfully = (args: string[], runCwd: string = cwd): string => {
+  const result = runSetup(args, runCwd);
+  if (result.status !== 0) {
+    throw new Error(
+      result.stderr || result.error?.message || `Exited with ${result.status}`,
+    );
+  }
+  return `${result.stdout}${result.stderr}`;
+};
+
 beforeEach(() => {
   cwd = mkdtempSync(path.join(import.meta.dirname, 'test-temp-rstack setup '));
   env = {
@@ -108,6 +119,65 @@ test('installs hooks silently without loading Rstack config', ({
   expect(execCli('setup', { cwd, env })).toBe('');
 });
 
+test('guides and forces setup while preserving existing hooks', ({
+  expect,
+}) => {
+  initRepository();
+  const existingHook = path.join(cwd, '.git', 'hooks', 'pre-commit');
+  writeFileSync(
+    existingHook,
+    "#!/usr/bin/env sh\nprintf 'ran\\n' > old-hook-ran\n",
+  );
+  chmodSync(existingHook, 0o755);
+
+  const skippedOutput = runSetupSuccessfully([]);
+  expect(skippedOutput).toContain(
+    'Git hooks setup skipped: existing Git hooks were found: pre-commit.',
+  );
+  expect(skippedOutput).toContain(
+    'To continue, run rs setup --force. Existing hook files will be preserved but become inactive.',
+  );
+
+  const forcedOutput = runSetupSuccessfully(['--force']);
+  expect(forcedOutput).toContain(
+    'The previous Git hooks path ".git/hooks" is now inactive: pre-commit.',
+  );
+  expect(forcedOutput).toContain(
+    'The existing files were preserved and will become active again if core.hooksPath is unset.',
+  );
+  expect(git(['config', '--local', '--get', 'core.hooksPath'])).toBe(hooksPath);
+
+  git(['hook', 'run', 'pre-commit']);
+  expect(existsSync(path.join(cwd, 'old-hook-ran'))).toBe(false);
+
+  git(['config', '--local', '--unset', 'core.hooksPath']);
+  git(['hook', 'run', 'pre-commit']);
+  expect(existsSync(path.join(cwd, 'old-hook-ran'))).toBe(true);
+
+  expect(runSetupSuccessfully(['-f'])).toContain(
+    'The previous Git hooks path ".git/hooks" is now inactive: pre-commit.',
+  );
+});
+
+test('reports how to restore a replaced hooks path', ({ expect }) => {
+  initRepository();
+  const existingDirectory = path.join(cwd, '.husky', '_');
+  mkdirSync(existingDirectory, { recursive: true });
+  writeFileSync(
+    path.join(existingDirectory, 'pre-commit'),
+    '#!/usr/bin/env sh\n',
+  );
+  git(['config', '--local', 'core.hooksPath', '.husky/_']);
+
+  const output = runSetupSuccessfully(['--force']);
+  expect(output).toContain(
+    'The previous Git hooks path ".husky/_" is now inactive: pre-commit.',
+  );
+  expect(output).toContain(
+    'The existing files were preserved. Set core.hooksPath back to this path to use them again.',
+  );
+});
+
 test('installs root-relative hooks and reports owner conflicts', ({
   execCli,
   expect,
@@ -126,9 +196,7 @@ test('installs root-relative hooks and reports owner conflicts', ({
   );
   expect(existsSync(path.join(cwd, 'custom hooks', '_', 'runner'))).toBe(true);
 
-  const conflict = runSetup(['--hooks-dir', 'custom hooks'], docs);
-  expect(conflict.status).toBe(0);
-  expect(`${conflict.stdout}${conflict.stderr}`).toContain(
+  expect(runSetupSuccessfully(['--hooks-dir', 'custom hooks'], docs)).toContain(
     'Git hooks are already managed by Rstack project "frontend"',
   );
 });
diff --git a/packages/rstack/tests/setup/install.test.ts b/packages/rstack/tests/setup/install.test.ts
index f91b2b45..4a32fa80 100644
--- a/packages/rstack/tests/setup/install.test.ts
+++ b/packages/rstack/tests/setup/install.test.ts
@@ -137,8 +137,12 @@ test('reports Git configuration failures without changing hooksPath', () => {
   });
 });
 
-test('does not replace another Git hooks path', () => {
+test('requires force to replace another Git hooks path', () => {
   withRepository((cwd) => {
+    const existingDirectory = path.join(cwd, '.husky', '_');
+    const existingHook = path.join(existingDirectory, 'pre-commit');
+    mkdirSync(existingDirectory, { recursive: true });
+    writeFileSync(existingHook, '#!/usr/bin/env sh\n');
     runGit(cwd, ['config', '--local', 'core.hooksPath', '.husky/_']);
 
     expect(installHooks({ cwd })).toMatchObject({
@@ -149,10 +153,24 @@ test('does not replace another Git hooks path', () => {
       '.husky/_',
     );
     expect(existsSync(path.join(cwd, hooksPath))).toBe(false);
+
+    expect(installHooks({ cwd, force: true })).toEqual({
+      status: 'installed',
+      hooksPath,
+      inactiveHooks: {
+        hooks: ['pre-commit'],
+        path: '.husky/_',
+        restore: 'configure',
+      },
+    });
+    expect(runGit(cwd, ['config', '--local', '--get', 'core.hooksPath'])).toBe(
+      hooksPath,
+    );
+    expect(readFileSync(existingHook, 'utf8')).toBe('#!/usr/bin/env sh\n');
   });
 });
 
-test('does not bypass existing Git hooks', () => {
+test('requires force to bypass existing Git hooks', () => {
   withRepository((cwd) => {
     const existingHook = path.join(cwd, '.git', 'hooks', 'pre-commit');
     writeFileSync(existingHook, '#!/usr/bin/env sh\n');
@@ -165,6 +183,54 @@ test('does not bypass existing Git hooks', () => {
     expect(
       git(cwd, ['config', '--local', '--get', 'core.hooksPath']).status,
     ).toBe(1);
+
+    expect(installHooks({ cwd, force: true })).toEqual({
+      status: 'installed',
+      hooksPath,
+      inactiveHooks: {
+        hooks: ['pre-commit'],
+        path: '.git/hooks',
+        restore: 'unset',
+      },
+    });
+    expect(runGit(cwd, ['config', '--local', '--get', 'core.hooksPath'])).toBe(
+      hooksPath,
+    );
     expect(readFileSync(existingHook, 'utf8')).toBe('#!/usr/bin/env sh\n');
   });
 });
+
+test('force does not replace hooks owned by another Rstack project', () => {
+  withRepository((cwd) => {
+    const frontend = path.join(cwd, 'frontend');
+    const docs = path.join(cwd, 'docs');
+    mkdirSync(frontend);
+    mkdirSync(docs);
+
+    expect(installHooks({ cwd: frontend }).status).toBe('installed');
+    expect(installHooks({ cwd: docs, force: true })).toMatchObject({
+      status: 'skipped',
+      reason: 'owned-by-another-project',
+    });
+    expect(readFileSync(path.join(cwd, hooksPath, '.owner'), 'utf8')).toBe(
+      'frontend\n',
+    );
+  });
+});
+
+test('force does not replace an invalid Rstack hooks directory', () => {
+  withRepository((cwd) => {
+    const directory = path.join(cwd, hooksPath);
+    mkdirSync(directory, { recursive: true });
+    writeFileSync(path.join(directory, '.owner'), 'invalid');
+
+    expect(installHooks({ cwd, force: true })).toMatchObject({
+      status: 'skipped',
+      reason: 'hooks-directory-conflict',
+    });
+    expect(
+      git(cwd, ['config', '--local', '--get', 'core.hooksPath']).status,
+    ).toBe(1);
+    expect(existsSync(path.join(directory, 'runner'))).toBe(false);
+  });
+});