diff --git a/pre_commit/languages/node.py b/pre_commit/languages/node.py
index e7962cce..aac1c591 100644
--- a/pre_commit/languages/node.py
+++ b/pre_commit/languages/node.py
@@ -62,11 +62,13 @@ def install_environment(prefix, version, additional_dependencies):
             cmd.extend(['-n', version])
         cmd_output(*cmd)
 
-        dep = 'git+file:///{}'.format(prefix.prefix_dir)
         with in_env(prefix, version):
+            # https://npm.community/t/npm-install-g-git-vs-git-clone-cd-npm-install-g/5449
+            # install as if we installed from git
+            helpers.run_setup_cmd(prefix, ('npm', 'install'))
             helpers.run_setup_cmd(
                 prefix,
-                ('npm', 'install', '-g', dep) + additional_dependencies,
+                ('npm', 'install', '-g', '.') + additional_dependencies,
             )
 
 
diff --git a/pre_commit/store.py b/pre_commit/store.py
index 8301ecad..93a9cab3 100644
--- a/pre_commit/store.py
+++ b/pre_commit/store.py
@@ -10,6 +10,7 @@ import tempfile
 import pre_commit.constants as C
 from pre_commit import file_lock
 from pre_commit import git
+from pre_commit.util import CalledProcessError
 from pre_commit.util import clean_path_on_failure
 from pre_commit.util import cmd_output
 from pre_commit.util import resource_text
@@ -134,19 +135,43 @@ class Store(object):
                 )
         return directory
 
+    def _complete_clone(self, ref, git_cmd):
+        """Perform a complete clone of a repository and its submodules """
+
+        git_cmd('fetch', 'origin')
+        git_cmd('checkout', ref)
+        git_cmd('submodule', 'update', '--init', '--recursive')
+
+    def _shallow_clone(self, ref, git_cmd):  # pragma: windows no cover
+        """Perform a shallow clone of a repository and its submodules """
+
+        git_config = 'protocol.version=2'
+        git_cmd('-c', git_config, 'fetch', 'origin', ref, '--depth=1')
+        git_cmd('checkout', ref)
+        git_cmd(
+            '-c', git_config, 'submodule', 'update', '--init',
+            '--recursive', '--depth=1',
+        )
+
     def clone(self, repo, ref, deps=()):
         """Clone the given url and checkout the specific ref."""
+
+        if os.path.isdir(repo):
+            repo = os.path.abspath(repo)
+
         def clone_strategy(directory):
             env = git.no_git_env()
 
-            cmd = ('git', 'clone', '--no-checkout', repo, directory)
-            cmd_output(*cmd, env=env)
-
             def _git_cmd(*args):
-                return cmd_output('git', *args, cwd=directory, env=env)
+                cmd_output('git', *args, cwd=directory, env=env)
 
-            _git_cmd('reset', ref, '--hard')
-            _git_cmd('submodule', 'update', '--init', '--recursive')
+            _git_cmd('init', '.')
+            _git_cmd('remote', 'add', 'origin', repo)
+
+            try:
+                self._shallow_clone(ref, _git_cmd)
+            except CalledProcessError:
+                self._complete_clone(ref, _git_cmd)
 
         return self._new_repo(repo, ref, deps, clone_strategy)
 
diff --git a/tests/store_test.py b/tests/store_test.py
index 238343fd..66217588 100644
--- a/tests/store_test.py
+++ b/tests/store_test.py
@@ -12,6 +12,7 @@ import six
 from pre_commit import git
 from pre_commit.store import _get_default_directory
 from pre_commit.store import Store
+from pre_commit.util import CalledProcessError
 from testing.fixtures import git_dir
 from testing.util import cwd
 from testing.util import git_commit
@@ -111,6 +112,41 @@ def test_clone_when_repo_already_exists(store):
     assert store.clone('fake_repo', 'fake_ref') == 'fake_path'
 
 
+def test_clone_shallow_failure_fallback_to_complete(
+    store, tempdir_factory,
+    log_info_mock,
+):
+    path = git_dir(tempdir_factory)
+    with cwd(path):
+        git_commit()
+        rev = git.head_rev(path)
+        git_commit()
+
+    # Force shallow clone failure
+    def fake_shallow_clone(self, *args, **kwargs):
+        raise CalledProcessError(None, None, None)
+    store._shallow_clone = fake_shallow_clone
+
+    ret = store.clone(path, rev)
+
+    # Should have printed some stuff
+    assert log_info_mock.call_args_list[0][0][0].startswith(
+        'Initializing environment for ',
+    )
+
+    # Should return a directory inside of the store
+    assert os.path.exists(ret)
+    assert ret.startswith(store.directory)
+    # Directory should start with `repo`
+    _, dirname = os.path.split(ret)
+    assert dirname.startswith('repo')
+    # Should be checked out to the rev we specified
+    assert git.head_rev(ret) == rev
+
+    # Assert there's an entry in the sqlite db for this
+    assert store.select_all_repos() == [(path, rev, ret)]
+
+
 def test_create_when_directory_exists_but_not_db(store):
     # In versions <= 0.3.5, there was no sqlite db causing a need for
     # backward compatibility