diff --git a/bootstrap.py b/bootstrap.py
index 00375cac33724..7ed6823571fd8 100755
--- a/bootstrap.py
+++ b/bootstrap.py
@@ -23,25 +23,6 @@
 # created. Bootstrap.py needs to be run before an .emscripten config exists.
 from tools import utils
 
-actions = [
-  ('npm packages', [
-     'package.json',
-     'package-lock.json',
-   ], ['npm', 'ci']),
-  ('create entry points', [
-     'tools/maint/create_entry_points.py',
-     'tools/pylauncher/pylauncher.exe',
-     'tools/maint/run_python.bat',
-     'tools/maint/run_python.sh',
-     'tools/maint/run_python.ps1',
-   ], [sys.executable, 'tools/maint/create_entry_points.py']),
-  ('git submodules', [
-     'test/third_party/posixtestsuite/',
-     'test/third_party/googletest',
-     'test/third_party/wasi-test-suite',
-   ], ['git', 'submodule', 'update', '--init']),
-]
-
 
 def get_stamp_file(action_name):
   return os.path.join(STAMP_DIR, action_name.replace(' ', '_') + '.stamp')
@@ -64,44 +45,110 @@ def check():
       utils.exit_with_error(f'emscripten setup is not complete ("{name}" is out-of-date). Run `bootstrap.py` to update')
 
 
+def ask_yes_no(question):
+  while True:
+    try:
+      reply = input(f"{question} (y/n): ").strip().lower()
+    except EOFError:
+      return False
+
+    if reply in {'y', 'yes'}:
+      return True
+    if reply in {'n', 'no'}:
+      return False
+
+    print("Invalid input. Please enter 'y' or 'n'.")
+
+
+def maybe_install_hooks():
+  if os.path.exists('.git/hooks/pre-push'):
+    print('git hooks already installed; skipping')
+    return
+  if os.environ.get('CI') or not sys.stdin.isatty():
+    # Do nothing when running in CI or non-interactive shell
+    return
+  if ask_yes_no('Install emscripten git hooks (see tools/maint/git-hooks)?'):
+    install_hooks()
+
+
+def install_hooks():
+  if not os.path.exists(utils.path_from_root('.git')):
+    print('--install-git-hooks requires a git checkout')
+    return 1
+
+  dst = utils.path_from_root('.git/hooks')
+  if not os.path.exists(dst):
+    os.mkdir(dst)
+
+  for src in ('tools/maint/git-hooks/post-checkout', 'tools/maint/git-hooks/pre-push'):
+    shutil.copy(utils.path_from_root(src), dst)
+  return 0
+
+
+def run_cmd(cmd):
+  orig_exe = cmd[0]
+  if not os.path.isabs(orig_exe):
+    cmd[0] = shutil.which(orig_exe)
+    if not cmd[0]:
+      utils.exit_with_error(f'command not found: {orig_exe}')
+  print(' -> %s' % ' '.join(cmd))
+  subprocess.run(cmd, check=True, text=True, encoding='utf-8', cwd=utils.path_from_root())
+
+
+actions = [
+  ('npm packages', [
+     'package.json',
+     'package-lock.json',
+   ], ['npm', 'ci']),
+  ('create entry points', [
+     'tools/maint/create_entry_points.py',
+     'tools/pylauncher/pylauncher.exe',
+     'tools/maint/run_python.bat',
+     'tools/maint/run_python.sh',
+     'tools/maint/run_python.ps1',
+   ], [sys.executable, 'tools/maint/create_entry_points.py']),
+  ('git submodules', [
+     'test/third_party/posixtestsuite/',
+     'test/third_party/googletest',
+     'test/third_party/wasi-test-suite',
+   ], ['git', 'submodule', 'update', '--init']),
+  ('install hooks', [
+     'tools/maint/git-hooks/post-checkout',
+     'tools/maint/git-hooks/pre-push',
+   ], maybe_install_hooks),
+]
+
+
 def main(args):
   parser = argparse.ArgumentParser(description=__doc__)
   parser.add_argument('-v', '--verbose', action='store_true', help='verbose', default=False)
+  parser.add_argument('-f', '--force', action='store_true', help='force all actions to run', default=False)
   parser.add_argument('-n', '--dry-run', action='store_true', help='dry run', default=False)
   parser.add_argument('-i', '--install-git-hooks', action='store_true', help='install emscripten git hooks', default=False)
   args = parser.parse_args()
 
   if args.install_git_hooks:
-    if not os.path.exists(utils.path_from_root('.git')):
-      print('--install-git-hooks requires git checkout')
-      return 1
-
-    dst = utils.path_from_root('.git/hooks')
-    if not os.path.exists(dst):
-      os.mkdir(dst)
-
-    src = utils.path_from_root('tools/maint/post-checkout')
-    for src in ('tools/maint/post-checkout', 'tools/maint/pre-push'):
-      shutil.copy(utils.path_from_root(src), dst)
-    return 0
-
-  for name, deps, cmd in actions:
-    if check_deps(name, deps):
-      print('Up-to-date: %s' % name)
-      continue
-    print('Out-of-date: %s' % name)
-    stamp_file = get_stamp_file(name)
+    return install_hooks()
+
+  for name, deps, action in actions:
+    if not args.force:
+      if check_deps(name, deps):
+        print('Up-to-date: %s' % name)
+        continue
+      print('Out-of-date: %s' % name)
     if args.dry_run:
-      print(' (skipping: dry run) -> %s' % ' '.join(cmd))
+      if type(action) == list:
+        action_str = ' '.join(action)
+      else:
+        action_str = action.__name__
+      print(f' (skipping: dry run) -> {action_str}')
       continue
-    orig_exe = cmd[0]
-    if not os.path.isabs(orig_exe):
-      cmd[0] = shutil.which(orig_exe)
-      if not cmd[0]:
-        utils.exit_with_error(f'command not found: {orig_exe}')
-    print(' -> %s' % ' '.join(cmd))
-    subprocess.run(cmd, check=True, text=True, encoding='utf-8', cwd=utils.path_from_root())
+    if type(action) == list:
+      run_cmd(action)
+    else:
+      action()
     utils.safe_ensure_dirs(STAMP_DIR)
+    stamp_file = get_stamp_file(name)
     utils.write_file(stamp_file, 'Timestamp file created by bootstrap.py')
   return 0
 
diff --git a/tools/maint/post-checkout b/tools/maint/git-hooks/post-checkout
similarity index 88%
rename from tools/maint/post-checkout
rename to tools/maint/git-hooks/post-checkout
index af7e11f5b2ea6..d64ca612a7ef6 100755
--- a/tools/maint/post-checkout
+++ b/tools/maint/git-hooks/post-checkout
@@ -6,7 +6,7 @@
 # The bootstrap script itself is smart enough to basically do nothing unless
 # one of the relevant files was updated (e.g. package.json).
 #
-# This script can be installed using `bootstrap.py -i`.
+# This script is normally installed by `bootstrap.py`.
 
 # Test for the existence of the bootstrap script itself to handle branches
 # that predate its existence.
diff --git a/tools/maint/pre-push b/tools/maint/git-hooks/pre-push
similarity index 64%
rename from tools/maint/pre-push
rename to tools/maint/git-hooks/pre-push
index 37f28bea7e7af..0408735329590 100755
--- a/tools/maint/pre-push
+++ b/tools/maint/git-hooks/pre-push
@@ -2,7 +2,7 @@
 #
 # Git pre-push script that runs some quick/simple tests.
 #
-# This script can be installed using `bootstrap.py -i`.
+# This script is normally installed by `bootstrap.py`.
 
 set -o errexit