diff --git a/pre_commit/commands/run.py b/pre_commit/commands/run.py
index 8d11882c0..37f78f746 100644
--- a/pre_commit/commands/run.py
+++ b/pre_commit/commands/run.py
@@ -333,7 +333,7 @@ def run(
     stash = not args.all_files and not args.files
 
     # Check if we have unresolved merge conflict files and fail fast.
-    if _has_unmerged_paths():
+    if stash and _has_unmerged_paths():
         logger.error('Unmerged files.  Resolve before committing.')
         return 1
     if bool(args.from_ref) != bool(args.to_ref):
diff --git a/tests/commands/run_test.py b/tests/commands/run_test.py
index 3ae3b537c..ef865330f 100644
--- a/tests/commands/run_test.py
+++ b/tests/commands/run_test.py
@@ -536,6 +536,13 @@ def test_merge_conflict(cap_out, store, in_merge_conflict):
     assert b'Unmerged files.  Resolve before committing.' in printed
 
 
+def test_files_during_merge_conflict(cap_out, store, in_merge_conflict):
+    opts = run_opts(files=['placeholder'])
+    ret, printed = _do_run(cap_out, store, in_merge_conflict, opts)
+    assert ret == 0
+    assert b'Bash hook' in printed
+
+
 def test_merge_conflict_modified(cap_out, store, in_merge_conflict):
     # Touch another file so we have unstaged non-conflicting things
     assert os.path.exists('placeholder')