diff --git a/syncapi/streams/stream_sendtodevice.go b/syncapi/streams/stream_sendtodevice.go
index 6a18df506..31c6187cb 100644
--- a/syncapi/streams/stream_sendtodevice.go
+++ b/syncapi/streams/stream_sendtodevice.go
@@ -39,21 +39,13 @@ func (p *SendToDeviceStreamProvider) IncrementalSync(
 		return from
 	}
 
-	if len(events) > 0 {
-		// Clean up old send-to-device messages from before this stream position.
-		if err := p.DB.CleanSendToDeviceUpdates(req.Context, req.Device.UserID, req.Device.ID, from); err != nil {
-			req.Log.WithError(err).Error("p.DB.CleanSendToDeviceUpdates failed")
-			return from
-		}
-
-		// Add the updates into the sync response.
-		for _, event := range events {
-			// skip ignored user events
-			if _, ok := req.IgnoredUsers.List[event.Sender]; ok {
-				continue
-			}
-			req.Response.ToDevice.Events = append(req.Response.ToDevice.Events, event.SendToDeviceEvent)
+	// Add the updates into the sync response.
+	for _, event := range events {
+		// skip ignored user events
+		if _, ok := req.IgnoredUsers.List[event.Sender]; ok {
+			continue
 		}
+		req.Response.ToDevice.Events = append(req.Response.ToDevice.Events, event.SendToDeviceEvent)
 	}
 
 	return lastPos
diff --git a/syncapi/sync/requestpool.go b/syncapi/sync/requestpool.go
index b6b4779a5..d908a9629 100644
--- a/syncapi/sync/requestpool.go
+++ b/syncapi/sync/requestpool.go
@@ -25,6 +25,11 @@ import (
 	"sync"
 	"time"
 
+	"github.com/matrix-org/gomatrixserverlib"
+	"github.com/matrix-org/util"
+	"github.com/prometheus/client_golang/prometheus"
+	"github.com/sirupsen/logrus"
+
 	"github.com/matrix-org/dendrite/clientapi/jsonerror"
 	keyapi "github.com/matrix-org/dendrite/keyserver/api"
 	roomserverAPI "github.com/matrix-org/dendrite/roomserver/api"
@@ -35,10 +40,6 @@ import (
 	"github.com/matrix-org/dendrite/syncapi/streams"
 	"github.com/matrix-org/dendrite/syncapi/types"
 	userapi "github.com/matrix-org/dendrite/userapi/api"
-	"github.com/matrix-org/gomatrixserverlib"
-	"github.com/matrix-org/util"
-	"github.com/prometheus/client_golang/prometheus"
-	"github.com/sirupsen/logrus"
 )
 
 // RequestPool manages HTTP long-poll connections for /sync
@@ -251,6 +252,12 @@ func (rp *RequestPool) OnIncomingSyncRequest(req *http.Request, device *userapi.
 	waitingSyncRequests.Inc()
 	defer waitingSyncRequests.Dec()
 
+	// Clean up old send-to-device messages from before this stream position.
+	// This is needed to avoid sending the same message multiple times
+	if err = rp.db.CleanSendToDeviceUpdates(syncReq.Context, syncReq.Device.UserID, syncReq.Device.ID, syncReq.Since.SendToDevicePosition); err != nil {
+		syncReq.Log.WithError(err).Error("p.DB.CleanSendToDeviceUpdates failed")
+	}
+
 	// loop until we get some data
 	for {
 		startTime := time.Now()