diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index 80620d50af..845c702222 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -958,6 +958,7 @@ static int sparse_checkout_clean(int argc, const char **argv,
 	size_t worktree_len;
 	int force = 0, dry_run = 0, verbose = 0;
 	int require_force = 1;
+	struct unpack_trees_options o = { 0 };
 
 	struct option builtin_sparse_checkout_clean_options[] = {
 		OPT__DRY_RUN(&dry_run, N_("dry run")),
@@ -986,6 +987,13 @@ static int sparse_checkout_clean(int argc, const char **argv,
 	if (repo_read_index(repo) < 0)
 		die(_("failed to read index"));
 
+	o.verbose_update = verbose;
+	o.update = 0; /* skip modifying the worktree here. */
+	o.head_idx = -1;
+	o.src_index = o.dst_index = repo->index;
+	if (update_sparsity(&o, NULL))
+		warning(_("failed to reapply sparse-checkout patterns"));
+
 	if (convert_to_sparse(repo->index, SPARSE_INDEX_MEMORY_ONLY) ||
 	    repo->index->sparse_index == INDEX_EXPANDED)
 		die(_("failed to convert index to a sparse index; resolve merge conflicts and try again"));
diff --git a/t/t1091-sparse-checkout-builtin.sh b/t/t1091-sparse-checkout-builtin.sh
index 116ad7c9a2..4b9078d90a 100755
--- a/t/t1091-sparse-checkout-builtin.sh
+++ b/t/t1091-sparse-checkout-builtin.sh
@@ -1104,6 +1104,7 @@ test_expect_success 'clean with staged sparse change' '
 
 	cat >expect <<-\EOF &&
 	Would remove deep/deeper2/
+	Would remove folder1/
 	EOF
 
 	git -C repo sparse-checkout clean --dry-run >out &&
@@ -1115,6 +1116,7 @@ test_expect_success 'clean with staged sparse change' '
 	# deletes deep/deeper2/ but leaves folder1/ and folder2/
 	cat >expect <<-\EOF &&
 	Removing deep/deeper2/
+	Removing folder1/
 	EOF
 
 	# The previous test case checked the -f option, so
@@ -1124,7 +1126,7 @@ test_expect_success 'clean with staged sparse change' '
 	test_cmp expect out &&
 
 	test_path_is_missing repo/deep/deeper2 &&
-	test_path_exists repo/folder1 &&
+	test_path_is_missing repo/folder1 &&
 	test_path_exists repo/folder2
 '
 
@@ -1147,7 +1149,11 @@ test_expect_success 'sparse-checkout operations with merge conflicts' '
 		git commit -a -m "left" &&
 
 		git checkout -b merge &&
-		git sparse-checkout set deep/deeper1 &&
+
+		touch deep/deeper2/extra &&
+		git sparse-checkout set deep/deeper1 2>err &&
+		grep "contains untracked files" err &&
+		test_path_exists deep/deeper2/extra &&
 
 		test_must_fail git merge -m "will-conflict" right &&
 
@@ -1159,15 +1165,19 @@ test_expect_success 'sparse-checkout operations with merge conflicts' '
 		git merge --continue &&
 
 		test_path_exists folder1/even/more/dirs/file &&
+		test_path_exists deep/deeper2/extra &&
+
+		cat >expect <<-\EOF &&
+		Removing deep/deeper2/
+		Removing folder1/
+		EOF
 
 		# clean does not remove the file, because the
 		# SKIP_WORKTREE bit was not cleared by the merge command.
 		git sparse-checkout clean -f >out &&
-		test_line_count = 0 out &&
-		test_path_exists folder1/even/more/dirs/file &&
-
-		git sparse-checkout reapply &&
-		test_path_is_missing folder1
+		test_cmp expect out &&
+		test_path_is_missing folder1 &&
+		test_path_is_missing deep/deeper2
 	)
 '
 
diff --git a/unpack-trees.c b/unpack-trees.c
index f38c761ab9..3a5dc062d7 100644
--- a/unpack-trees.c
+++ b/unpack-trees.c
@@ -2138,7 +2138,7 @@ enum update_sparsity_result update_sparsity(struct unpack_trees_options *o,
 	index_state_init(&o->internal.result, o->src_index->repo);
 
 	/* Sanity checks */
-	if (!o->update || o->index_only || o->skip_sparse_checkout)
+	if (o->index_only || o->skip_sparse_checkout)
 		BUG("update_sparsity() is for reflecting sparsity patterns in working directory");
 	if (o->src_index != o->dst_index || o->fn)
 		BUG("update_sparsity() called wrong");