diff --git a/builtin/clone.c b/builtin/clone.c
index d60d1b60bc..9d08cd8722 100644
--- a/builtin/clone.c
+++ b/builtin/clone.c
@@ -1116,7 +1116,6 @@ int cmd_clone(int argc,
 			die_errno(_("could not create work tree dir '%s'"),
 				  work_tree);
 		junk_work_tree = work_tree;
-		set_git_work_tree(the_repository, work_tree);
 	}
 
 	if (real_git_dir) {
@@ -1186,9 +1185,10 @@ int cmd_clone(int argc,
 	 * repository, and reference backends may persist that information into
 	 * their on-disk data structures.
 	 */
-	init_db(the_repository, git_dir, real_git_dir, option_template, GIT_HASH_UNKNOWN,
-		ref_storage_format, NULL,
-		do_not_override_repo_unix_permissions, INIT_DB_QUIET | INIT_DB_SKIP_REFDB);
+	init_db(the_repository, git_dir, real_git_dir, work_tree, option_template,
+		GIT_HASH_UNKNOWN, ref_storage_format, NULL,
+		do_not_override_repo_unix_permissions,
+		INIT_DB_QUIET | INIT_DB_SKIP_REFDB);
 
 	if (real_git_dir) {
 		free((char *)git_dir);
diff --git a/builtin/init-db.c b/builtin/init-db.c
index 566732c9f4..e96b1283b7 100644
--- a/builtin/init-db.c
+++ b/builtin/init-db.c
@@ -231,39 +231,25 @@ int cmd_init_db(int argc,
 	if (!bare) {
 		const char *git_dir_parent = strrchr(git_dir, '/');
 
-		if (work_tree) {
-			set_git_work_tree(the_repository, work_tree);
-		} else {
-			char *work_tree_cfg = NULL;
-
+		if (!work_tree) {
 			if (git_dir_parent) {
 				char *rel = xstrndup(git_dir, git_dir_parent - git_dir);
-				work_tree_cfg = real_pathdup(rel, 1);
+				work_tree = real_pathdup(rel, 1);
 				free(rel);
+			} else {
+				work_tree = xgetcwd();
 			}
-
-			if (!work_tree_cfg)
-				work_tree_cfg = xgetcwd();
-
-			set_git_work_tree(the_repository, work_tree_cfg);
-
-			free(work_tree_cfg);
 		}
 
-		if (access(repo_get_work_tree(the_repository), X_OK))
-			die_errno (_("Cannot access work tree '%s'"),
-				   repo_get_work_tree(the_repository));
-	}
-	else {
-		if (real_git_dir)
-			die(_("--separate-git-dir incompatible with bare repository"));
-		if (work_tree)
-			set_git_work_tree(the_repository, work_tree);
+		if (access(work_tree, X_OK))
+			die_errno (_("Cannot access work tree '%s'"), work_tree);
+	} else if (real_git_dir) {
+		die(_("--separate-git-dir incompatible with bare repository"));
 	}
 
 	flags |= INIT_DB_EXIST_OK;
-	ret = init_db(the_repository, git_dir, real_git_dir, template_dir, hash_algo,
-		      ref_storage_format, initial_branch,
+	ret = init_db(the_repository, git_dir, real_git_dir, work_tree,
+		      template_dir, hash_algo, ref_storage_format, initial_branch,
 		      init_shared_repository, flags);
 
 	free(template_dir_to_free);
diff --git a/setup.c b/setup.c
index 088e7b85f7..683b8e65a2 100644
--- a/setup.c
+++ b/setup.c
@@ -2823,7 +2823,9 @@ static void repository_format_configure(struct repository_format *repo_fmt,
 }
 
 int init_db(struct repository *repo,
-	    const char *git_dir, const char *real_git_dir,
+	    const char *git_dir,
+	    const char *real_git_dir,
+	    const char *worktree,
 	    const char *template_dir, int hash,
 	    enum ref_storage_format ref_storage_format,
 	    const char *initial_branch,
@@ -2852,6 +2854,9 @@ int init_db(struct repository *repo,
 		git_dir = repo_get_git_dir(repo);
 	}
 
+	if (worktree)
+		set_git_work_tree(repo, worktree);
+
 	/*
 	 * Check to see if the repository version is right.
 	 * Note that a newly created repository does not have
diff --git a/setup.h b/setup.h
index c01a244fe9..bf3e3f3ea6 100644
--- a/setup.h
+++ b/setup.h
@@ -263,7 +263,9 @@ const char *get_template_dir(const char *option_template);
 #define INIT_DB_SKIP_REFDB (1 << 2)
 
 int init_db(struct repository *repo,
-	    const char *git_dir, const char *real_git_dir,
+	    const char *git_dir,
+	    const char *real_git_dir,
+	    const char *worktree,
 	    const char *template_dir, int hash_algo,
 	    enum ref_storage_format ref_storage_format,
 	    const char *initial_branch, int init_shared_repository,