diff --git a/tools/perf/builtin-config.c b/tools/perf/builtin-config.c
index 3ddcc6e2abeb..a1d82e33282c 100644
--- a/tools/perf/builtin-config.c
+++ b/tools/perf/builtin-config.c
@@ -59,7 +59,7 @@ static int set_config(struct perf_config_set *set, const char *file_name,
 		fprintf(fp, "[%s]\n", section->name);
 
 		perf_config_items__for_each_entry(&section->items, item) {
-			if (!use_system_config && section->from_system_config)
+			if (!use_system_config && item->from_system_config)
 				continue;
 			if (item->value)
 				fprintf(fp, "\t%s = %s\n",