diff --git a/src/merge.c b/src/merge.c
index a0f2405ff..b93851b7e 100644
--- a/src/merge.c
+++ b/src/merge.c
@@ -2827,6 +2827,7 @@ static int merge_check_workdir(size_t *conflicts, git_repository *repo, git_inde
 	opts.flags |= GIT_DIFF_DISABLE_PATHSPEC_MATCH;
 	opts.pathspec.count = merged_paths->length;
 	opts.pathspec.strings = (char **)merged_paths->contents;
+	opts.ignore_submodules = GIT_SUBMODULE_IGNORE_ALL;
 
 	if ((error = git_diff_index_to_workdir(&wd_diff_list, repo, NULL, &opts)) < 0)
 		goto done;