diff --git a/pre_commit/commands/autoupdate.py b/pre_commit/commands/autoupdate.py
index 9e1e79f2..a446a172 100644
--- a/pre_commit/commands/autoupdate.py
+++ b/pre_commit/commands/autoupdate.py
@@ -69,6 +69,7 @@ def autoupdate(runner):
 
     for repo_config in input_configs:
         if is_local_hooks(repo_config):
+            output_configs.append(repo_config)
             continue
         sys.stdout.write('Updating {0}...'.format(repo_config['repo']))
         sys.stdout.flush()
diff --git a/testing/fixtures.py b/testing/fixtures.py
index 820a72be..a311b20e 100644
--- a/testing/fixtures.py
+++ b/testing/fixtures.py
@@ -68,9 +68,11 @@ def make_config_from_repo(repo_path, sha=None, hooks=None, check=True):
 
 
 def write_config(directory, config):
-    assert type(config) is OrderedDict
+    if type(config) is not list:
+        assert type(config) is OrderedDict
+        config = [config]
     with io.open(os.path.join(directory, C.CONFIG_FILE), 'w') as config_file:
-        config_file.write(ordered_dump([config], **C.YAML_DUMP_KWARGS))
+        config_file.write(ordered_dump(config, **C.YAML_DUMP_KWARGS))
 
 
 def add_config_to_repo(git_path, config):
diff --git a/tests/commands/autoupdate_test.py b/tests/commands/autoupdate_test.py
index 771e67b1..f067a16c 100644
--- a/tests/commands/autoupdate_test.py
+++ b/tests/commands/autoupdate_test.py
@@ -5,6 +5,7 @@ import shutil
 import pytest
 
 import pre_commit.constants as C
+from pre_commit.clientlib.validate_config import load_config
 from pre_commit.commands.autoupdate import _update_repository
 from pre_commit.commands.autoupdate import autoupdate
 from pre_commit.commands.autoupdate import RepositoryCannotBeUpdatedError
@@ -146,4 +147,24 @@ def test_autoupdate_local_hooks(tmpdir_factory):
     git_path = git_dir(tmpdir_factory)
     config = config_with_local_hooks()
     path = add_config_to_repo(git_path, config)
-    assert autoupdate(Runner(path)) == 0
+    runner = Runner(path)
+    assert autoupdate(runner) == 0
+    new_config_writen = load_config(runner.config_file_path)
+    assert len(new_config_writen) == 1
+    assert new_config_writen[0] == config
+
+
+def test_autoupdate_local_hooks_with_out_of_date_repo(
+        out_of_date_repo, in_tmpdir, mock_out_store_directory
+):
+    stale_config = make_config_from_repo(
+        out_of_date_repo.path, sha=out_of_date_repo.original_sha, check=False,
+    )
+    local_config = config_with_local_hooks()
+    config = [local_config, stale_config]
+    write_config('.', config)
+    runner = Runner('.')
+    assert autoupdate(runner) == 0
+    new_config_writen = load_config(runner.config_file_path)
+    assert len(new_config_writen) == 2
+    assert new_config_writen[0] == local_config