diff --git a/tools/perf/builtin-config.c b/tools/perf/builtin-config.c
index 7c861b54f3a6..8c0d93b7c2f0 100644
--- a/tools/perf/builtin-config.c
+++ b/tools/perf/builtin-config.c
@@ -48,14 +48,18 @@ static int set_config(struct perf_config_set *set, const char *file_name,
 	if (!fp)
 		return -1;
 
-	perf_config_set__collect(set, var, value);
+	perf_config_set__collect(set, file_name, var, value);
 	fprintf(fp, "%s\n", first_line);
 
 	/* overwrite configvariables */
 	perf_config_items__for_each_entry(&set->sections, section) {
+		if (!use_system_config && section->from_system_config)
+			continue;
 		fprintf(fp, "[%s]\n", section->name);
 
 		perf_config_items__for_each_entry(&section->items, item) {
+			if (!use_system_config && section->from_system_config)
+				continue;
 			if (item->value)
 				fprintf(fp, "\t%s = %s\n",
 					item->name, item->value);
diff --git a/tools/perf/util/config.c b/tools/perf/util/config.c
index c8fb65d923cb..3d906dbbef74 100644
--- a/tools/perf/util/config.c
+++ b/tools/perf/util/config.c
@@ -594,6 +594,19 @@ static int collect_config(const char *var, const char *value,
 			goto out_free;
 	}
 
+	/* perf_config_set can contain both user and system config items.
+	 * So we should know where each value is from.
+	 * The classification would be needed when a particular config file
+	 * is overwrited by setting feature i.e. set_config().
+	 */
+	if (strcmp(config_file_name, perf_etc_perfconfig()) == 0) {
+		section->from_system_config = true;
+		item->from_system_config = true;
+	} else {
+		section->from_system_config = false;
+		item->from_system_config = false;
+	}
+
 	ret = set_value(item, value);
 	return ret;
 
@@ -602,9 +615,10 @@ out_free:
 	return -1;
 }
 
-int perf_config_set__collect(struct perf_config_set *set,
+int perf_config_set__collect(struct perf_config_set *set, const char *file_name,
 			     const char *var, const char *value)
 {
+	config_file_name = file_name;
 	return collect_config(var, value, set);
 }
 
diff --git a/tools/perf/util/config.h b/tools/perf/util/config.h
index 0fcdb8c594b0..1a59a6b43f8b 100644
--- a/tools/perf/util/config.h
+++ b/tools/perf/util/config.h
@@ -7,12 +7,14 @@
 struct perf_config_item {
 	char *name;
 	char *value;
+	bool from_system_config;
 	struct list_head node;
 };
 
 struct perf_config_section {
 	char *name;
 	struct list_head items;
+	bool from_system_config;
 	struct list_head node;
 };
 
@@ -33,7 +35,7 @@ const char *perf_etc_perfconfig(void);
 
 struct perf_config_set *perf_config_set__new(void);
 void perf_config_set__delete(struct perf_config_set *set);
-int perf_config_set__collect(struct perf_config_set *set,
+int perf_config_set__collect(struct perf_config_set *set, const char *file_name,
 			     const char *var, const char *value);
 void perf_config__init(void);
 void perf_config__exit(void);