diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index a4bdd7c4940260..f1b856c8e0f76c 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -15,6 +15,7 @@
 #include "wt-status.h"
 #include "quote.h"
 #include "sparse-index.h"
+#include "run-command.h"
 
 static const char *empty_base = "";
 
@@ -100,6 +101,71 @@ static int sparse_checkout_list(int argc, const char **argv)
 	return 0;
 }
 
+static void clean_tracked_sparse_directories(struct repository *r)
+{
+	int i;
+	struct strvec args = STRVEC_INIT;
+
+	/*
+	 * If we are not using cone mode patterns, then we cannot
+	 * delete directories outside of the sparse cone.
+	 */
+	if (!r || !r->index || !r->index->sparse_checkout_patterns ||
+	    !r->index->sparse_checkout_patterns->use_cone_patterns)
+		return;
+	/*
+	 * NEEDSWORK: For now, only use this behavior when index.sparse
+	 * is enabled. We may want this behavior enabled whenever using
+	 * cone mode patterns.
+	 */
+	prepare_repo_settings(r);
+	if (!r->settings.sparse_index)
+		return;
+
+	strvec_pushl(&args, "clean", "-dfx", NULL);
+
+	/*
+	 * Since we now depend on the sparse index to enable this
+	 * behavior, use it to our advantage. This process is more
+	 * complicated without it.
+	 */
+	convert_to_sparse(r->index);
+
+	for (i = 0; i < r->index->cache_nr; i++) {
+		struct cache_entry *ce = r->index->cache[i];
+
+		/*
+		 * Is this a sparse directory? If so, then definitely
+		 * include it. All contained content is outside of the
+		 * patterns.
+		 */
+		if (S_ISSPARSEDIR(ce->ce_mode) &&
+		    repo_file_exists(r, ce->name)) {
+			strvec_push(&args, ce->name);
+			continue;
+		}
+	}
+
+	run_command_v_opt(args.v, RUN_GIT_CMD);
+
+	/*
+	 * The 'git clean -dfx -- <path> ...' command empties the
+	 * tracked directories outside of the sparse cone, but does not
+	 * delete the directories themselves. Remove them now.
+	 */
+	for (i = 2; i < args.nr; i++)
+		rmdir_or_warn(args.v[i]);
+
+	strvec_clear(&args);
+
+	/*
+	 * This is temporary: the sparse-checkout builtin is not
+	 * integrated with the sparse-index yet, so we need to keep
+	 * it full during the process.
+	 */
+	ensure_full_index(r->index);
+}
+
 static int update_working_directory(struct pattern_list *pl)
 {
 	enum update_sparsity_result result;
@@ -141,6 +207,8 @@ static int update_working_directory(struct pattern_list *pl)
 	else
 		rollback_lock_file(&lock_file);
 
+	clean_tracked_sparse_directories(r);
+
 	r->index->sparse_checkout_patterns = NULL;
 	return result;
 }
@@ -540,8 +608,11 @@ static int modify_pattern_list(int argc, const char **argv, enum modify_type m)
 {
 	int result;
 	int changed_config = 0;
+	struct pattern_list *old_pl = xcalloc(1, sizeof(*old_pl));
 	struct pattern_list *pl = xcalloc(1, sizeof(*pl));
 
+	get_sparse_checkout_patterns(old_pl);
+
 	switch (m) {
 	case ADD:
 		if (core_sparse_checkout_cone)
@@ -567,7 +638,9 @@ static int modify_pattern_list(int argc, const char **argv, enum modify_type m)
 		set_config(MODE_NO_PATTERNS);
 
 	clear_pattern_list(pl);
+	clear_pattern_list(old_pl);
 	free(pl);
+	free(old_pl);
 	return result;
 }
 
diff --git a/t/t1091-sparse-checkout-builtin.sh b/t/t1091-sparse-checkout-builtin.sh
index 92613f381c7d23..ef1567b75be11c 100755
--- a/t/t1091-sparse-checkout-builtin.sh
+++ b/t/t1091-sparse-checkout-builtin.sh
@@ -642,4 +642,42 @@ test_expect_success MINGW 'cone mode replaces backslashes with slashes' '
 	check_files repo/deep a deeper1
 '
 
+test_expect_success 'cone mode clears ignored subdirectories' '
+	rm repo/.git/info/sparse-checkout &&
+
+	# NEEDSWORK: --sparse-index is required for now
+	git -C repo sparse-checkout init --cone --sparse-index &&
+	git -C repo sparse-checkout set deep/deeper1 &&
+
+	cat >repo/.gitignore <<-\EOF &&
+	obj/
+	*.o
+	EOF
+
+	git -C repo add .gitignore &&
+	git -C repo commit -m ".gitignore" &&
+
+	for dir in  folder1 obj folder1/obj deep/deeper2 deep/deeper2/obj
+	do
+		mkdir repo/$dir || return 1
+	done &&
+	for file in folder1/obj/a obj/a folder1/file.o folder1.o \
+		    deep/deeper2/obj/a deep/deeper2/file.o file.o
+	do
+		echo ignored >repo/$file || return 1
+	done &&
+
+	git -C repo status --porcelain=v2 >out &&
+	test_must_be_empty out &&
+
+	git -C repo sparse-checkout reapply &&
+	test_path_is_missing repo/folder1 &&
+	test_path_is_missing repo/deep/deeper2 &&
+	test_path_is_dir repo/obj &&
+	test_path_is_file repo/file.o &&
+
+	git -C repo status --porcelain=v2 >out &&
+	test_must_be_empty out
+'
+
 test_done
diff --git a/t/t1092-sparse-checkout-compatibility.sh b/t/t1092-sparse-checkout-compatibility.sh
index dd3b72afc769f6..5635d62ca9ae50 100755
--- a/t/t1092-sparse-checkout-compatibility.sh
+++ b/t/t1092-sparse-checkout-compatibility.sh
@@ -594,7 +594,7 @@ test_expect_success 'sparse-index is not expanded' '
 	ensure_not_expanded add .
 '
 
-test_expect_failure 'sparse-index is not expanded (with ignored files outside cone)' '
+test_expect_success 'sparse-index is not expanded (with ignored files outside cone)' '
 	init_repos &&
 
 	write_script adjust_repo <<-\EOF &&
@@ -606,6 +606,7 @@ test_expect_failure 'sparse-index is not expanded (with ignored files outside co
 	EOF
 
 	run_on_all ../adjust_repo &&
+	git -C sparse-index sparse-checkout reapply &&
 
 	ensure_not_expanded status &&
 	ensure_not_expanded commit --allow-empty -m empty &&
@@ -622,14 +623,7 @@ test_expect_failure 'sparse-index is not expanded (with ignored files outside co
 	git -C sparse-index reset --hard &&
 	ensure_not_expanded checkout rename-out-to-out -- deep/deeper1 &&
 	git -C sparse-index reset --hard &&
-	ensure_not_expanded restore -s rename-out-to-out -- deep/deeper1 &&
-
-	echo >>sparse-index/README.md &&
-	ensure_not_expanded add -A &&
-	echo >>sparse-index/extra.txt &&
-	ensure_not_expanded add extra.txt &&
-	echo >>sparse-index/untracked.txt &&
-	ensure_not_expanded add .
+	ensure_not_expanded restore -s rename-out-to-out -- deep/deeper1
 '
 
 test_expect_success 'reset mixed and checkout orphan' '