diff --git a/builtin/submodule--helper.c b/builtin/submodule--helper.c
index d2ab31835b..0be737ac4f 100644
--- a/builtin/submodule--helper.c
+++ b/builtin/submodule--helper.c
@@ -1810,12 +1810,12 @@ static int clone_submodule(const struct module_clone_data *clone_data,
 	/* setup alternateLocation and alternateErrorStrategy in the cloned submodule if needed */
 	repo_config_get_string(the_repository, "submodule.alternateLocation", &sm_alternate);
 	if (sm_alternate)
-		git_config_set_in_file(p, "submodule.alternateLocation",
-				       sm_alternate);
+		repo_config_set_in_file(the_repository, p, "submodule.alternateLocation",
+					sm_alternate);
 	repo_config_get_string(the_repository, "submodule.alternateErrorStrategy", &error_strategy);
 	if (error_strategy)
-		git_config_set_in_file(p, "submodule.alternateErrorStrategy",
-				       error_strategy);
+		repo_config_set_in_file(the_repository, p, "submodule.alternateErrorStrategy",
+					error_strategy);
 
 	free(sm_alternate);
 	free(error_strategy);
@@ -2522,7 +2522,7 @@ static int ensure_core_worktree(const char *path)
 		abs_path = absolute_pathdup(path);
 		rel_path = relative_path(abs_path, subrepo.gitdir, &sb);
 
-		git_config_set_in_file(cfg_file, "core.worktree", rel_path);
+		repo_config_set_in_file(the_repository, cfg_file, "core.worktree", rel_path);
 
 		free(cfg_file);
 		free(abs_path);
diff --git a/config.h b/config.h
index c9f582c7c5..b4f79d4d4c 100644
--- a/config.h
+++ b/config.h
@@ -734,12 +734,6 @@ static inline int git_config_get_pathname(const char *key, char **dest)
 	return repo_config_get_pathname(the_repository, key, dest);
 }
 
-static inline void git_config_set_in_file(const char *config_filename,
-					  const char *key, const char *value)
-{
-	repo_config_set_in_file(the_repository, config_filename, key, value);
-}
-
 static inline int git_config_set_gently(const char *key, const char *value)
 {
 	return repo_config_set_gently(the_repository, key, value);
diff --git a/dir.c b/dir.c
index 02873f59ea..dfb4d40103 100644
--- a/dir.c
+++ b/dir.c
@@ -4091,8 +4091,8 @@ void connect_work_tree_and_git_dir(const char *work_tree_,
 	write_file(gitfile_sb.buf, "gitdir: %s",
 		   relative_path(git_dir, work_tree, &rel_path));
 	/* Update core.worktree setting */
-	git_config_set_in_file(cfg_sb.buf, "core.worktree",
-			       relative_path(work_tree, git_dir, &rel_path));
+	repo_config_set_in_file(the_repository, cfg_sb.buf, "core.worktree",
+				relative_path(work_tree, git_dir, &rel_path));
 
 	strbuf_release(&gitfile_sb);
 	strbuf_release(&cfg_sb);