diff --git a/builtin/sparse-checkout.c b/builtin/sparse-checkout.c
index fb85a1459c..3f828feb1f 100644
--- a/builtin/sparse-checkout.c
+++ b/builtin/sparse-checkout.c
@@ -684,6 +684,28 @@ static int modify_pattern_list(int argc, const char **argv, int use_stdin,
 	return result;
 }
 
+static void sanitize_paths(int argc, const char **argv, const char *prefix)
+{
+	if (!argc)
+		return;
+
+	if (prefix && *prefix && core_sparse_checkout_cone) {
+		/*
+		 * The args are not pathspecs, so unfortunately we
+		 * cannot imitate how cmd_add() uses parse_pathspec().
+		 */
+		int i;
+		int prefix_len = strlen(prefix);
+
+		for (i = 0; i < argc; i++)
+			argv[i] = prefix_path(prefix, prefix_len, argv[i]);
+	}
+
+	if (prefix && *prefix && !core_sparse_checkout_cone)
+		die(_("please run from the toplevel directory in non-cone mode"));
+
+}
+
 static char const * const builtin_sparse_checkout_add_usage[] = {
 	N_("git sparse-checkout add (--stdin | <patterns>)"),
 	NULL
@@ -711,6 +733,8 @@ static int sparse_checkout_add(int argc, const char **argv, const char *prefix)
 			     builtin_sparse_checkout_add_usage,
 			     PARSE_OPT_KEEP_UNKNOWN);
 
+	sanitize_paths(argc, argv, prefix);
+
 	return modify_pattern_list(argc, argv, add_opts.use_stdin, ADD);
 }
 
@@ -762,6 +786,8 @@ static int sparse_checkout_set(int argc, const char **argv, const char *prefix)
 	if (!core_sparse_checkout_cone && argc == 0) {
 		argv = default_patterns;
 		argc = default_patterns_nr;
+	} else {
+		sanitize_paths(argc, argv, prefix);
 	}
 
 	return modify_pattern_list(argc, argv, set_opts.use_stdin, REPLACE);
diff --git a/t/t1091-sparse-checkout-builtin.sh b/t/t1091-sparse-checkout-builtin.sh
index ce5e7c19ef..c1f86b0e02 100755
--- a/t/t1091-sparse-checkout-builtin.sh
+++ b/t/t1091-sparse-checkout-builtin.sh
@@ -798,4 +798,45 @@ test_expect_success 'malformed cone-mode patterns' '
 	grep "warning: disabling cone pattern matching" err
 '
 
+test_expect_success 'set from subdir pays attention to prefix' '
+	git -C repo sparse-checkout disable &&
+	git -C repo/deep sparse-checkout set --cone deeper2 ../folder1 &&
+
+	git -C repo sparse-checkout list >actual &&
+
+	cat >expect <<-\EOF &&
+	deep/deeper2
+	folder1
+	EOF
+	test_cmp expect actual
+'
+
+test_expect_success 'add from subdir pays attention to prefix' '
+	git -C repo sparse-checkout set --cone deep/deeper2 &&
+	git -C repo/deep sparse-checkout add deeper1/deepest ../folder1 &&
+
+	git -C repo sparse-checkout list >actual &&
+
+	cat >expect <<-\EOF &&
+	deep/deeper1/deepest
+	deep/deeper2
+	folder1
+	EOF
+	test_cmp expect actual
+'
+
+test_expect_success 'set from subdir in non-cone mode throws an error' '
+	git -C repo sparse-checkout disable &&
+	test_must_fail git -C repo/deep sparse-checkout set --no-cone deeper2 ../folder1 2>error &&
+
+	grep "run from the toplevel directory in non-cone mode" error
+'
+
+test_expect_success 'set from subdir in non-cone mode throws an error' '
+	git -C repo sparse-checkout set --no-cone deep/deeper2 &&
+	test_must_fail git -C repo/deep sparse-checkout add deeper1/deepest ../folder1 2>error &&
+
+	grep "run from the toplevel directory in non-cone mode" error
+'
+
 test_done