diff --git a/builtin/submodule--helper.c b/builtin/submodule--helper.c
index 20ae9191ca..216e3daf5c 100644
--- a/builtin/submodule--helper.c
+++ b/builtin/submodule--helper.c
@@ -1124,6 +1124,8 @@ static void deinit_submodule(const char *path, const char *prefix,
 		if (!(flags & OPT_QUIET))
 			printf(format, displaypath);
 
+		submodule_unset_core_worktree(sub);
+
 		strbuf_release(&sb_rm);
 	}
 
@@ -2004,6 +2006,29 @@ static int check_name(int argc, const char **argv, const char *prefix)
 	return 0;
 }
 
+static int connect_gitdir_workingtree(int argc, const char **argv, const char *prefix)
+{
+	struct strbuf sb = STRBUF_INIT;
+	const char *name, *path;
+	char *sm_gitdir;
+
+	if (argc != 3)
+		BUG("submodule--helper connect-gitdir-workingtree <name> <path>");
+
+	name = argv[1];
+	path = argv[2];
+
+	strbuf_addf(&sb, "%s/modules/%s", get_git_dir(), name);
+	sm_gitdir = absolute_pathdup(sb.buf);
+
+	connect_work_tree_and_git_dir(path, sm_gitdir, 0);
+
+	strbuf_release(&sb);
+	free(sm_gitdir);
+
+	return 0;
+}
+
 #define SUPPORT_SUPER_PREFIX (1<<0)
 
 struct cmd_struct {
@@ -2017,6 +2042,7 @@ static struct cmd_struct commands[] = {
 	{"name", module_name, 0},
 	{"clone", module_clone, 0},
 	{"update-clone", update_clone, 0},
+	{"connect-gitdir-workingtree", connect_gitdir_workingtree, 0},
 	{"relative-path", resolve_relative_path, 0},
 	{"resolve-relative-url", resolve_relative_url, 0},
 	{"resolve-relative-url-test", resolve_relative_url_test, 0},
diff --git a/git-submodule.sh b/git-submodule.sh
index 5f9d9f6ea3..8b5ad59bde 100755
--- a/git-submodule.sh
+++ b/git-submodule.sh
@@ -577,6 +577,11 @@ cmd_update()
 			die "$(eval_gettext "Unable to find current \${remote_name}/\${branch} revision in submodule path '\$sm_path'")"
 		fi
 
+		if ! $(git config -f "$(git rev-parse --git-common-dir)/modules/$name/config" core.worktree) 2>/dev/null
+		then
+			git submodule--helper connect-gitdir-workingtree "$name" "$sm_path"
+		fi
+
 		if test "$subsha1" != "$sha1" || test -n "$force"
 		then
 			subforce=$force
diff --git a/submodule.c b/submodule.c
index 0998ea2345..d3a9aab83d 100644
--- a/submodule.c
+++ b/submodule.c
@@ -1534,6 +1534,18 @@ int bad_to_remove_submodule(const char *path, unsigned flags)
 	return ret;
 }
 
+void submodule_unset_core_worktree(const struct submodule *sub)
+{
+	char *config_path = xstrfmt("%s/modules/%s/config",
+				    get_git_common_dir(), sub->name);
+
+	if (git_config_set_in_file_gently(config_path, "core.worktree", NULL))
+		warning(_("Could not unset core.worktree setting in submodule '%s'"),
+			  sub->path);
+
+	free(config_path);
+}
+
 static const char *get_super_prefix_or_empty(void)
 {
 	const char *s = get_super_prefix();
@@ -1699,6 +1711,8 @@ int submodule_move_head(const char *path,
 
 			if (is_empty_dir(path))
 				rmdir_or_warn(path);
+
+			submodule_unset_core_worktree(sub);
 		}
 	}
 out:
diff --git a/submodule.h b/submodule.h
index 7856b8a0b3..4644683e6c 100644
--- a/submodule.h
+++ b/submodule.h
@@ -121,6 +121,8 @@ extern int submodule_move_head(const char *path,
 			       const char *new_head,
 			       unsigned flags);
 
+void submodule_unset_core_worktree(const struct submodule *sub);
+
 /*
  * Prepare the "env_array" parameter of a "struct child_process" for executing
  * a submodule by clearing any repo-specific environment variables, but
diff --git a/t/lib-submodule-update.sh b/t/lib-submodule-update.sh
index 1f38a85371..aa5ac03325 100755
--- a/t/lib-submodule-update.sh
+++ b/t/lib-submodule-update.sh
@@ -235,7 +235,7 @@ reset_work_tree_to_interested () {
 	then
 		mkdir -p submodule_update/.git/modules/sub1/modules &&
 		cp -r submodule_update_repo/.git/modules/sub1/modules/sub2 submodule_update/.git/modules/sub1/modules/sub2
-		GIT_WORK_TREE=. git -C submodule_update/.git/modules/sub1/modules/sub2 config --unset core.worktree
+		# core.worktree is unset for sub2 as it is not checked out
 	fi &&
 	# indicate we are interested in the submodule:
 	git -C submodule_update config submodule.sub1.url "bogus" &&
@@ -709,7 +709,8 @@ test_submodule_recursing_with_args_common() {
 			git branch -t remove_sub1 origin/remove_sub1 &&
 			$command remove_sub1 &&
 			test_superproject_content origin/remove_sub1 &&
-			! test -e sub1
+			! test -e sub1 &&
+			test_must_fail git config -f .git/modules/sub1/config core.worktree
 		)
 	'
 	# ... absorbing a .git directory along the way.
diff --git a/t/t7400-submodule-basic.sh b/t/t7400-submodule-basic.sh
index 812db137b8..48fd14fae6 100755
--- a/t/t7400-submodule-basic.sh
+++ b/t/t7400-submodule-basic.sh
@@ -993,6 +993,11 @@ test_expect_success 'submodule deinit should remove the whole submodule section
 	rmdir init
 '
 
+test_expect_success 'submodule deinit should unset core.worktree' '
+	test_path_is_file .git/modules/example/config &&
+	test_must_fail git config -f .git/modules/example/config core.worktree
+'
+
 test_expect_success 'submodule deinit from subdirectory' '
 	git submodule update --init &&
 	git config submodule.example.foo bar &&