diff --git a/pre_commit/commands/autoupdate.py b/pre_commit/commands/autoupdate.py
index 844c6017..4dce674f 100644
--- a/pre_commit/commands/autoupdate.py
+++ b/pre_commit/commands/autoupdate.py
@@ -98,7 +98,7 @@ def _write_new_config_file(path, output):
     # If we failed to intelligently rewrite the sha lines, fall back to the
     # pretty-formatted yaml output
     to_write = ''.join(lines)
-    if ordered_load(to_write) != output:
+    if remove_defaults(ordered_load(to_write), CONFIG_SCHEMA) != output:
         to_write = new_contents
 
     with open(path, 'w') as f:
diff --git a/tests/commands/autoupdate_test.py b/tests/commands/autoupdate_test.py
index 7fb21b9d..2877c5b3 100644
--- a/tests/commands/autoupdate_test.py
+++ b/tests/commands/autoupdate_test.py
@@ -275,7 +275,7 @@ def test_autoupdate_local_hooks(tempdir_factory):
     runner = Runner(path, C.CONFIG_FILE)
     assert autoupdate(runner, tags_only=False) == 0
     new_config_writen = load_config(runner.config_file_path)
-    assert len(new_config_writen) == 1
+    assert len(new_config_writen['repos']) == 1
     assert new_config_writen['repos'][0] == config