diff --git a/ChangeLog.txt b/ChangeLog.txt
index b2ce7b9e..36a3d868 100644
--- a/ChangeLog.txt
+++ b/ChangeLog.txt
@@ -8,6 +8,8 @@ Broker:
 - Fix include_dir not sorting config files before loading. This was partially
   fixed in 1.5 previously.
 - Improve documentation around the `include_dir` option. Closes #1154.
+- Fix case where old unreferenced msg_store messages were being saved to the
+  persistence file, bloating its size unnecessarily. Closes #389.
 
 Library:
 - Fix `mosquitto_topic_matches_sub()` not returning MOSQ_ERR_INVAL for
diff --git a/src/database.c b/src/database.c
index 8253cb41..6596dd23 100644
--- a/src/database.c
+++ b/src/database.c
@@ -235,6 +235,21 @@ void db__msg_store_deref(struct mosquitto_db *db, struct mosquitto_msg_store **s
 }
 
 
+void db__msg_store_compact(struct mosquitto_db *db)
+{
+	struct mosquitto_msg_store *store, *next;
+
+	store = db->msg_store;
+	while(store){
+		next = store->next;
+		if(store->ref_count < 1){
+			db__msg_store_remove(db, store);
+		}
+		store = next;
+	}
+}
+
+
 static void db__message_remove(struct mosquitto_db *db, struct mosquitto *context, struct mosquitto_client_msg **msg, struct mosquitto_client_msg *last)
 {
 	if(!context || !msg || !(*msg)){
@@ -1019,8 +1034,3 @@ void db__limits_set(int inflight, unsigned long inflight_bytes, int queued, unsi
 	max_queued_bytes = queued_bytes;
 }
 
-void db__vacuum(void)
-{
-	/* FIXME - reimplement? */
-}
-
diff --git a/src/mosquitto_broker_internal.h b/src/mosquitto_broker_internal.h
index 31305841..db96f1f9 100644
--- a/src/mosquitto_broker_internal.h
+++ b/src/mosquitto_broker_internal.h
@@ -562,8 +562,8 @@ void db__msg_store_add(struct mosquitto_db *db, struct mosquitto_msg_store *stor
 void db__msg_store_remove(struct mosquitto_db *db, struct mosquitto_msg_store *store);
 void db__msg_store_deref(struct mosquitto_db *db, struct mosquitto_msg_store **store);
 void db__msg_store_clean(struct mosquitto_db *db);
+void db__msg_store_compact(struct mosquitto_db *db);
 int db__message_reconnect_reset(struct mosquitto_db *db, struct mosquitto *context);
-void db__vacuum(void);
 void sys_tree__init(struct mosquitto_db *db);
 void sys_tree__update(struct mosquitto_db *db, int interval, time_t start_time);
 
diff --git a/src/persist.c b/src/persist.c
index 13b34d2c..abce7e9a 100644
--- a/src/persist.c
+++ b/src/persist.c
@@ -151,6 +151,11 @@ static int persist__message_store_write(struct mosquitto_db *db, FILE *db_fptr)
 
 	stored = db->msg_store;
 	while(stored){
+		if(stored->ref_count < 1){
+			stored = stored->next;
+			continue;
+		}
+
 		if(stored->topic && !strncmp(stored->topic, "$SYS", 4)){
 			if(stored->ref_count <= 1 && stored->dest_id_count == 0){
 				/* $SYS messages that are only retained shouldn't be persisted. */
@@ -982,6 +987,9 @@ int persist__restore(struct mosquitto_db *db)
 		HASH_DELETE(hh, db->msg_store_load, load);
 		mosquitto__free(load);
 	}
+
+	db__msg_store_compact(db);
+
 	return rc;
 error:
 	err = strerror(errno);