diff --git a/pre_commit/commands/run.py b/pre_commit/commands/run.py
index 56450e38..508b61a3 100644
--- a/pre_commit/commands/run.py
+++ b/pre_commit/commands/run.py
@@ -258,7 +258,9 @@ def _all_filenames(args: argparse.Namespace) -> Collection[str]:
 
 
 def _get_diff() -> bytes:
-    _, out, _ = cmd_output_b('git', 'diff', '--no-ext-diff', retcode=None)
+    _, out, _ = cmd_output_b(
+        'git', 'diff', '--no-ext-diff', '--ignore-submodules', retcode=None,
+    )
     return out
 
 
diff --git a/pre_commit/git.py b/pre_commit/git.py
index 13ba664c..8e22dcf0 100644
--- a/pre_commit/git.py
+++ b/pre_commit/git.py
@@ -130,7 +130,9 @@ def get_staged_files(cwd: Optional[str] = None) -> List[str]:
 
 
 def intent_to_add_files() -> List[str]:
-    _, stdout, _ = cmd_output('git', 'status', '--porcelain', '-z')
+    _, stdout, _ = cmd_output(
+        'git', 'status', '--ignore-submodules', '--porcelain', '-z',
+    )
     parts = list(reversed(zsplit(stdout)))
     intent_to_add = []
     while parts: