diff --git a/builtin/init-db.c b/builtin/init-db.c
index bbc9bc78f9..7b915d88ab 100644
--- a/builtin/init-db.c
+++ b/builtin/init-db.c
@@ -9,6 +9,7 @@
 #include "builtin.h"
 #include "exec-cmd.h"
 #include "parse-options.h"
+#include "worktree.h"
 
 #ifndef DEFAULT_GIT_TEMPLATE_DIR
 #define DEFAULT_GIT_TEMPLATE_DIR "/usr/share/git-core/templates"
@@ -364,6 +365,7 @@ static void separate_git_dir(const char *git_dir, const char *git_link)
 
 		if (rename(src, git_dir))
 			die_errno(_("unable to move %s to %s"), src, git_dir);
+		repair_worktrees(NULL, NULL);
 	}
 
 	write_file(git_link, "gitdir: %s", git_dir);
diff --git a/t/t0001-init.sh b/t/t0001-init.sh
index 50222a10c5..e489eb4ddb 100755
--- a/t/t0001-init.sh
+++ b/t/t0001-init.sh
@@ -405,6 +405,17 @@ test_expect_success SYMLINKS 're-init to move gitdir symlink' '
 	test_path_is_dir realgitdir/refs
 '
 
+test_expect_success 're-init to move gitdir with linked worktrees' '
+	test_when_finished "rm -rf mainwt linkwt seprepo" &&
+	git init mainwt &&
+	test_commit -C mainwt gumby &&
+	git -C mainwt worktree add --detach ../linkwt &&
+	git -C mainwt init --separate-git-dir ../seprepo &&
+	git -C mainwt rev-parse --git-common-dir >expect &&
+	git -C linkwt rev-parse --git-common-dir >actual &&
+	test_cmp expect actual
+'
+
 test_expect_success MINGW '.git hidden' '
 	rm -rf newdir &&
 	(