diff --git a/pre_commit/commands/autoupdate.py b/pre_commit/commands/autoupdate.py
index 8f3714c4..d93d7e11 100644
--- a/pre_commit/commands/autoupdate.py
+++ b/pre_commit/commands/autoupdate.py
@@ -4,6 +4,7 @@ from __future__ import unicode_literals
 import re
 from collections import OrderedDict
 
+import six
 from aspy.yaml import ordered_dump
 from aspy.yaml import ordered_load
 from cfgv import remove_defaults
@@ -11,6 +12,7 @@ from cfgv import remove_defaults
 import pre_commit.constants as C
 from pre_commit import output
 from pre_commit.clientlib import CONFIG_SCHEMA
+from pre_commit.clientlib import InvalidManifestError
 from pre_commit.clientlib import is_local_repo
 from pre_commit.clientlib import is_meta_repo
 from pre_commit.clientlib import load_config
@@ -53,11 +55,15 @@ def _update_repo(repo_config, store, tags_only):
     # Construct a new config with the head rev
     new_config = OrderedDict(repo_config)
     new_config['rev'] = rev
-    new_repo = Repository.create(new_config, store)
+
+    try:
+        new_hooks = Repository.create(new_config, store).manifest_hooks
+    except InvalidManifestError as e:
+        raise RepositoryCannotBeUpdatedError(six.text_type(e))
 
     # See if any of our hooks were deleted with the new commits
     hooks = {hook['id'] for hook in repo_config['hooks']}
-    hooks_missing = hooks - (hooks & set(new_repo.manifest_hooks))
+    hooks_missing = hooks - set(new_hooks)
     if hooks_missing:
         raise RepositoryCannotBeUpdatedError(
             'Cannot update because the tip of master is missing these hooks:\n'
diff --git a/tests/commands/autoupdate_test.py b/tests/commands/autoupdate_test.py
index 3bfb62e0..b6e81b2a 100644
--- a/tests/commands/autoupdate_test.py
+++ b/tests/commands/autoupdate_test.py
@@ -260,6 +260,21 @@ def test_autoupdate_tags_only(tagged_repo_with_more_commits, in_tmpdir, store):
         assert 'v1.2.3' in f.read()
 
 
+def test_autoupdate_latest_no_config(out_of_date_repo, in_tmpdir, store):
+    config = make_config_from_repo(
+        out_of_date_repo.path, rev=out_of_date_repo.original_rev,
+    )
+    write_config('.', config)
+
+    cmd_output('git', '-C', out_of_date_repo.path, 'rm', '-r', ':/')
+    cmd_output('git', '-C', out_of_date_repo.path, 'commit', '-m', 'rm')
+
+    ret = autoupdate(Runner('.', C.CONFIG_FILE), store, tags_only=False)
+    assert ret == 1
+    with open(C.CONFIG_FILE) as f:
+        assert out_of_date_repo.original_rev in f.read()
+
+
 @pytest.fixture
 def hook_disappearing_repo(tempdir_factory):
     path = make_repo(tempdir_factory, 'python_hooks_repo')