diff --git a/bootstrap.py b/bootstrap.py
index 858ddf734448..695ae528b212 100755
--- a/bootstrap.py
+++ b/bootstrap.py
@@ -20,11 +20,15 @@
 from tools import shared, utils
 
 actions = [
-  ('npm packages', 'package.json', [shutil.which('npm'), 'ci']),
-  # TODO(sbc): Remove the checked in entry point files and have them
-  # built on demand by this step.
-  ('create entry points', 'tools/maint/create_entry_points.py', [sys.executable, 'tools/maint/create_entry_points.py']),
-  ('git submodules', 'test/third_party/posixtestsuite/', [shutil.which('git'), 'submodule', 'update', '--init']),
+  ('npm packages', ['package.json'], [shutil.which('npm'), 'ci']),
+  ('create entry points', [
+     'tools/maint/create_entry_points.py',
+     '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/'], [shutil.which('git'), 'submodule', 'update', '--init']),
 ]
 
 
@@ -32,12 +36,21 @@ def get_stamp_file(action_name):
   return os.path.join(STAMP_DIR, action_name.replace(' ', '_') + '.stamp')
 
 
+def check_deps(name, deps):
+  stamp_file = get_stamp_file(name)
+  if not os.path.exists(stamp_file):
+    return False
+  for dep in deps:
+    dep = utils.path_from_root(dep)
+    if os.path.getmtime(dep) > os.path.getmtime(stamp_file):
+      return False
+  return True
+
+
 def check():
-  for name, filename, _ in actions:
-    stamp_file = get_stamp_file(name)
-    filename = utils.path_from_root(filename)
-    if not os.path.exists(stamp_file) or os.path.getmtime(filename) > os.path.getmtime(stamp_file):
-      utils.exit_with_error(f'emscripten setup is not complete ("{name}" is out-of-date). Run bootstrap.py to update')
+  for name, deps, _ in actions:
+    if not check_deps(name, deps):
+      utils.exit_with_error(f'emscripten setup is not complete ("{name}" is out-of-date). Run `bootstrap` to update')
 
 
 def main(args):
@@ -46,13 +59,12 @@ def main(args):
   parser.add_argument('-n', '--dry-run', action='store_true', help='dry run', default=False)
   args = parser.parse_args()
 
-  for name, filename, cmd in actions:
-    stamp_file = get_stamp_file(name)
-    filename = utils.path_from_root(filename)
-    if os.path.exists(stamp_file) and os.path.getmtime(filename) <= os.path.getmtime(stamp_file):
+  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)
     if args.dry_run:
       print(' (skipping: dry run) -> %s' % ' '.join(cmd))
       return
diff --git a/test/test_sanity.py b/test/test_sanity.py
index 942469ae7a28..8ff59d68d275 100644
--- a/test/test_sanity.py
+++ b/test/test_sanity.py
@@ -757,7 +757,7 @@ def test_bootstrap(self):
     # Touching package.json should cause compiler to fail with bootstrap message
     Path(utils.path_from_root('package.json')).touch()
     err = self.expect_fail([EMCC, test_file('hello_world.c')])
-    self.assertContained('emcc: error: emscripten setup is not complete ("npm packages" is out-of-date). Run bootstrap.py to update', err)
+    self.assertContained('emcc: error: emscripten setup is not complete ("npm packages" is out-of-date). Run `bootstrap` to update', err)
 
     # Running bootstrap.py should fix that
     bootstrap = shared.bat_suffix(shared.path_from_root('bootstrap'))