diff --git a/pkg/ingester/flush.go b/pkg/ingester/flush.go
index 9e6bb9bd3d8ff2391db1820b062904d394f0d01f..23a7d27a0d8e268ee97fe11bdba0f01e01936292 100644
--- a/pkg/ingester/flush.go
+++ b/pkg/ingester/flush.go
@@ -204,6 +204,7 @@ func (i *Ingester) removeFlushedChunks(instance *instance, stream *stream) {
 
 	if len(stream.chunks) == 0 {
 		delete(instance.streams, stream.fp)
+		instance.index.Delete(stream.labels, stream.fp)
 		instance.streamsRemovedTotal.Inc()
 	}
 }