diff --git a/builtin/submodule--helper.c b/builtin/submodule--helper.c
index dffc55ed8e..1948090268 100644
--- a/builtin/submodule--helper.c
+++ b/builtin/submodule--helper.c
@@ -980,6 +980,8 @@ 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);
 	}
 
diff --git a/t/lib-submodule-update.sh b/t/lib-submodule-update.sh
index 12cd4e9233..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" &&
diff --git a/t/t7400-submodule-basic.sh b/t/t7400-submodule-basic.sh
index 2f532529b8..1a33040d94 100755
--- a/t/t7400-submodule-basic.sh
+++ b/t/t7400-submodule-basic.sh
@@ -991,6 +991,11 @@ 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 &&