diff --git a/federationsender/queue/destinationqueue.go b/federationsender/queue/destinationqueue.go
index 3ab939c68..c30567250 100644
--- a/federationsender/queue/destinationqueue.go
+++ b/federationsender/queue/destinationqueue.go
@@ -255,7 +255,7 @@ func (oq *destinationQueue) backgroundSend() {
 			}
 
 			// Try sending the next transaction and see what happens.
-			transaction, terr := oq.nextTransaction(transactionID, oq.pendingPDUs, oq.pendingEDUs, oq.statistics.SuccessCount())
+			transaction, terr := oq.nextTransaction(transactionID, oq.pendingPDUs, oq.pendingEDUs)
 			if terr != nil {
 				// We failed to send the transaction.
 				if giveUp := oq.statistics.Failure(); giveUp {
@@ -328,7 +328,6 @@ func (oq *destinationQueue) nextTransaction(
 	transactionID gomatrixserverlib.TransactionID,
 	pendingPDUs []*gomatrixserverlib.HeaderedEvent,
 	pendingEDUs []*gomatrixserverlib.EDU,
-	sentCounter uint32,
 ) (bool, error) {
 	t := gomatrixserverlib.Transaction{
 		PDUs: []json.RawMessage{},
diff --git a/federationsender/storage/postgres/queue_json_table.go b/federationsender/storage/postgres/queue_json_table.go
index 0f6ebe2ae..1095c6ad4 100644
--- a/federationsender/storage/postgres/queue_json_table.go
+++ b/federationsender/storage/postgres/queue_json_table.go
@@ -83,10 +83,10 @@ func (s *queueJSONStatements) insertQueueJSON(
 }
 
 func (s *queueJSONStatements) deleteQueueJSON(
-	ctx context.Context, txn *sql.Tx, eventIDs []string,
+	ctx context.Context, txn *sql.Tx, nids []int64,
 ) error {
 	stmt := sqlutil.TxStmt(txn, s.deleteJSONStmt)
-	_, err := stmt.ExecContext(ctx, pq.StringArray(eventIDs))
+	_, err := stmt.ExecContext(ctx, pq.Int64Array(nids))
 	return err
 }
 
diff --git a/federationsender/storage/postgres/queue_pdus_table.go b/federationsender/storage/postgres/queue_pdus_table.go
index 4ba22bc20..4e8b9f7e9 100644
--- a/federationsender/storage/postgres/queue_pdus_table.go
+++ b/federationsender/storage/postgres/queue_pdus_table.go
@@ -56,11 +56,16 @@ const selectQueuePDUsByTransactionSQL = "" +
 	" WHERE server_name = $1 AND transaction_id = $2" +
 	" LIMIT $3"
 
+const selectQueueReferenceJSONCountSQL = "" +
+	"SELECT COUNT(*) FROM federationsender_queue_pdus" +
+	" WHERE json_nid = $1"
+
 type queuePDUsStatements struct {
-	insertQueuePDUStmt               *sql.Stmt
-	deleteQueueTransactionPDUsStmt   *sql.Stmt
-	selectQueueNextTransactionIDStmt *sql.Stmt
-	selectQueuePDUsByTransactionStmt *sql.Stmt
+	insertQueuePDUStmt                *sql.Stmt
+	deleteQueueTransactionPDUsStmt    *sql.Stmt
+	selectQueueNextTransactionIDStmt  *sql.Stmt
+	selectQueuePDUsByTransactionStmt  *sql.Stmt
+	selectQueueReferenceJSONCountStmt *sql.Stmt
 }
 
 func (s *queuePDUsStatements) prepare(db *sql.DB) (err error) {
@@ -80,6 +85,9 @@ func (s *queuePDUsStatements) prepare(db *sql.DB) (err error) {
 	if s.selectQueuePDUsByTransactionStmt, err = db.Prepare(selectQueuePDUsByTransactionSQL); err != nil {
 		return
 	}
+	if s.selectQueueReferenceJSONCountStmt, err = db.Prepare(selectQueueReferenceJSONCountSQL); err != nil {
+		return
+	}
 	return
 }
 
@@ -112,8 +120,8 @@ func (s *queuePDUsStatements) deleteQueueTransaction(
 
 func (s *queuePDUsStatements) selectQueueNextTransactionID(
 	ctx context.Context, txn *sql.Tx, serverName gomatrixserverlib.ServerName,
-) (string, error) {
-	var transactionID string
+) (gomatrixserverlib.TransactionID, error) {
+	var transactionID gomatrixserverlib.TransactionID
 	stmt := sqlutil.TxStmt(txn, s.selectQueueNextTransactionIDStmt)
 	err := stmt.QueryRowContext(ctx, serverName).Scan(&transactionID)
 	if err == sql.ErrNoRows {
@@ -122,8 +130,23 @@ func (s *queuePDUsStatements) selectQueueNextTransactionID(
 	return transactionID, err
 }
 
+func (s *queuePDUsStatements) selectQueueReferenceJSONCount(
+	ctx context.Context, txn *sql.Tx, jsonNID int64,
+) (int64, error) {
+	var count int64
+	stmt := sqlutil.TxStmt(txn, s.selectQueueNextTransactionIDStmt)
+	err := stmt.QueryRowContext(ctx, jsonNID).Scan(&count)
+	if err == sql.ErrNoRows {
+		return -1, nil
+	}
+	return count, err
+}
+
 func (s *queuePDUsStatements) selectQueuePDUs(
-	ctx context.Context, txn *sql.Tx, serverName string, transactionID string, limit int,
+	ctx context.Context, txn *sql.Tx,
+	serverName gomatrixserverlib.ServerName,
+	transactionID gomatrixserverlib.TransactionID,
+	limit int,
 ) ([]int64, error) {
 	stmt := sqlutil.TxStmt(txn, s.selectQueuePDUsByTransactionStmt)
 	rows, err := stmt.QueryContext(ctx, serverName, transactionID, limit)
diff --git a/federationsender/storage/postgres/storage.go b/federationsender/storage/postgres/storage.go
index fb69a2f0f..b90ac874a 100644
--- a/federationsender/storage/postgres/storage.go
+++ b/federationsender/storage/postgres/storage.go
@@ -186,7 +186,7 @@ func (d *Database) GetNextTransactionPDUs(
 		return "", nil, nil
 	}
 
-	nids, err := d.selectQueuePDUs(ctx, nil, string(serverName), transactionID, limit)
+	nids, err := d.selectQueuePDUs(ctx, nil, serverName, transactionID, limit)
 	if err != nil {
 		return "", nil, fmt.Errorf("d.selectQueuePDUs: %w", err)
 	}
@@ -216,5 +216,32 @@ func (d *Database) CleanTransactionPDUs(
 	serverName gomatrixserverlib.ServerName,
 	transactionID gomatrixserverlib.TransactionID,
 ) error {
-	return d.deleteQueueTransaction(ctx, nil, serverName, transactionID)
+	nids, err := d.selectQueuePDUs(ctx, nil, serverName, transactionID, 50)
+	if err != nil {
+		return fmt.Errorf("d.selectQueuePDUs: %w", err)
+	}
+
+	if err = d.deleteQueueTransaction(ctx, nil, serverName, transactionID); err != nil {
+		return fmt.Errorf("d.deleteQueueTransaction: %w", err)
+	}
+
+	var count int64
+	var deleteNIDs []int64
+	for _, nid := range nids {
+		count, err = d.selectQueueReferenceJSONCount(ctx, nil, nid)
+		if err != nil {
+			return fmt.Errorf("d.selectQueueReferenceJSONCount: %w", err)
+		}
+		if count == 0 {
+			deleteNIDs = append(deleteNIDs, nid)
+		}
+	}
+
+	if len(deleteNIDs) > 0 {
+		if err = d.deleteQueueJSON(ctx, nil, deleteNIDs); err != nil {
+			return fmt.Errorf("d.deleteQueueJSON: %w", err)
+		}
+	}
+
+	return nil
 }