diff --git a/server/jetstream_cluster.go b/server/jetstream_cluster.go
index fef9958add4..51b9e504da9 100644
--- a/server/jetstream_cluster.go
+++ b/server/jetstream_cluster.go
@@ -1141,17 +1141,24 @@ type recoveryUpdates struct {
 // Streams and consumers are recovered from disk, and the meta layer's mappings
 // should clean them up, but under crash scenarios there could be orphans.
 func (js *jetStream) checkForOrphans() {
-	consumerName := func(o *consumer) string {
-		o.mu.RLock()
-		defer o.mu.RUnlock()
-		return o.name
-	}
-
 	// Can not hold jetstream lock while trying to delete streams or consumers.
 	js.mu.Lock()
 	s, cc := js.srv, js.cluster
 	s.Debugf("JetStream cluster checking for orphans")
 
+	// We only want to cleanup any orphans if we know we are current with the meta-leader.
+	meta := cc.meta
+	if meta == nil || meta.GroupLeader() == _EMPTY_ {
+		js.mu.Unlock()
+		s.Debugf("JetStream cluster skipping check for orphans, no meta-leader")
+		return
+	}
+	if !meta.Healthy() {
+		js.mu.Unlock()
+		s.Debugf("JetStream cluster skipping check for orphans, not current with the meta-leader")
+		return
+	}
+
 	var streams []*stream
 	var consumers []*consumer
 
@@ -1164,8 +1171,7 @@ func (js *jetStream) checkForOrphans() {
 			} else {
 				// This one is good, check consumers now.
 				for _, o := range mset.getConsumers() {
-					consumer := consumerName(o)
-					if sa.consumers[consumer] == nil {
+					if sa.consumers[o.String()] == nil {
 						consumers = append(consumers, o)
 					}
 				}
@@ -1369,7 +1375,7 @@ func (js *jetStream) monitorCluster() {
 					// Clear.
 					ru = nil
 					s.Debugf("Recovered JetStream cluster metadata")
-					js.checkForOrphans()
+					time.AfterFunc(30*time.Second, js.checkForOrphans)
 					// Do a health check here as well.
 					go checkHealth()
 					continue
diff --git a/server/jetstream_cluster_4_test.go b/server/jetstream_cluster_4_test.go
index c97cd64838a..4a0152e312d 100644
--- a/server/jetstream_cluster_4_test.go
+++ b/server/jetstream_cluster_4_test.go
@@ -1373,6 +1373,7 @@ func TestJetStreamClusterConsumerNRGCleanup(t *testing.T) {
 				numStreams++
 			}
 		}
+		f.Close()
 	}
 	require_Equal(t, numConsumers, 0)
 	require_Equal(t, numStreams, 0)
@@ -2493,3 +2494,58 @@ func TestJetStreamClusterWQRoundRobinSubjectRetention(t *testing.T) {
 	require_Equal(t, si.State.NumDeleted, 20)
 	require_Equal(t, si.State.NumSubjects, 4)
 }
+
+func TestJetStreamClusterMetaSyncOrphanCleanup(t *testing.T) {
+	c := createJetStreamClusterWithTemplateAndModHook(t, jsClusterTempl, "R3S", 3,
+		func(serverName, clusterName, storeDir, conf string) string {
+			return fmt.Sprintf("%s\nserver_tags: [server:%s]", conf, serverName)
+		})
+	defer c.shutdown()
+
+	nc, js := jsClientConnect(t, c.randomServer())
+	defer nc.Close()
+
+	// Create a bunch of streams on S1
+	for i := 0; i < 100; i++ {
+		stream := fmt.Sprintf("TEST-%d", i)
+		subject := fmt.Sprintf("TEST.%d", i)
+		_, err := js.AddStream(&nats.StreamConfig{
+			Name:      stream,
+			Subjects:  []string{subject},
+			Storage:   nats.FileStorage,
+			Placement: &nats.Placement{Tags: []string{"server:S-1"}},
+		})
+		require_NoError(t, err)
+		// Put in 10 msgs to each
+		for j := 0; j < 10; j++ {
+			_, err := js.Publish(subject, nil)
+			require_NoError(t, err)
+		}
+	}
+
+	// Now we will shutdown S1 and remove all of its meta-data to trip the condition.
+	s := c.serverByName("S-1")
+	require_True(t, s != nil)
+
+	sd := s.JetStreamConfig().StoreDir
+	nd := filepath.Join(sd, "$SYS", "_js_", "_meta_")
+	s.Shutdown()
+	s.WaitForShutdown()
+	os.RemoveAll(nd)
+	s = c.restartServer(s)
+	c.waitOnServerCurrent(s)
+	jsz, err := s.Jsz(nil)
+	require_NoError(t, err)
+	require_Equal(t, jsz.Streams, 100)
+
+	// These will be recreated by the meta layer, but if the orphan detection deleted them they will be empty,
+	// so check all streams to make sure they still have data.
+	acc := s.GlobalAccount()
+	var state StreamState
+	for i := 0; i < 100; i++ {
+		mset, err := acc.lookupStream(fmt.Sprintf("TEST-%d", i))
+		require_NoError(t, err)
+		mset.store.FastState(&state)
+		require_Equal(t, state.Msgs, 10)
+	}
+}