diff --git a/Documentation/config/index.txt b/Documentation/config/index.txt
index 23c7985eb40974..404e7bd37f80f3 100644
--- a/Documentation/config/index.txt
+++ b/Documentation/config/index.txt
@@ -1,3 +1,9 @@
+index.deleteSparseDirectories::
+	When enabled, the cone mode sparse-checkout feature will delete
+	directories that are outside of the sparse-checkout cone, unless
+	such a directory contains an untracked, non-ignored file. Defaults
+	to true.
+
 index.recordEndOfIndexEntries::
 	Specifies whether the index file should include an "End Of Index
 	Entry" section. This reduces index load time on multiprocessor
diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index 5c8ffb1f7598b0..75295951eb7974 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -111,7 +111,7 @@ static int sparse_checkout_list(int argc, const char **argv, const char *prefix)
 
 static void clean_tracked_sparse_directories(struct repository *r)
 {
-	int i, was_full = 0;
+	int i, value, was_full = 0;
 	struct strbuf path = STRBUF_INIT;
 	size_t pathlen;
 	struct string_list_item *item;
@@ -127,6 +127,13 @@ static void clean_tracked_sparse_directories(struct repository *r)
 	    !r->index->sparse_checkout_patterns->use_cone_patterns)
 		return;
 
+	/*
+	 * Users can disable this behavior.
+	 */
+	if (!repo_config_get_bool(r, "index.deletesparsedirectories", &value) &&
+	    !value)
+		return;
+
 	/*
 	 * Use the sparse index as a data structure to assist finding
 	 * directories that are safe to delete. This conversion to a
diff --git a/diff.c b/diff.c
index ee3eb629e3dc5e..9797ad009ceb68 100644
--- a/diff.c
+++ b/diff.c
@@ -3994,6 +3994,13 @@ static int reuse_worktree_file(struct index_state *istate,
 	if (!FAST_WORKING_DIRECTORY && !want_file && has_object_pack(oid))
 		return 0;
 
+	/*
+	 * If this path does not match our sparse-checkout definition,
+	 * then the file will not be in the working directory.
+	 */
+	if (!path_in_sparse_checkout(name, istate))
+		return 0;
+
 	/*
 	 * Similarly, if we'd have to convert the file contents anyway, that
 	 * makes the optimization not worthwhile.
diff --git a/t/t1091-sparse-checkout-builtin.sh b/t/t1091-sparse-checkout-builtin.sh
index 9ceb17f9118919..8a9ae66d578fda 100755
--- a/t/t1091-sparse-checkout-builtin.sh
+++ b/t/t1091-sparse-checkout-builtin.sh
@@ -782,6 +782,10 @@ test_expect_success 'cone mode clears ignored subdirectories' '
 	git -C repo status --porcelain=v2 >out &&
 	test_must_be_empty out &&
 
+	git -C repo -c index.deleteSparseDirectories=false sparse-checkout reapply &&
+	test_path_is_dir repo/folder1 &&
+	test_path_is_dir repo/deep/deeper2 &&
+
 	git -C repo sparse-checkout reapply &&
 	test_path_is_missing repo/folder1 &&
 	test_path_is_missing repo/deep/deeper2 &&