diff --git a/tsdb/wal/checkpoint.go b/tsdb/wal/checkpoint.go
index 8d3cc8ab6..6b0ecd54f 100644
--- a/tsdb/wal/checkpoint.go
+++ b/tsdb/wal/checkpoint.go
@@ -133,6 +133,10 @@ func Checkpoint(w *WAL, from, to int, keep func(id uint64) bool, mint int64) (*C
 	cpdir := filepath.Join(w.Dir(), fmt.Sprintf(checkpointPrefix+"%06d", to))
 	cpdirtmp := cpdir + ".tmp"
 
+	if err := os.RemoveAll(cpdirtmp); err != nil {
+		return nil, errors.Wrap(err, "remove previous temporary checkpoint dir")
+	}
+
 	if err := os.MkdirAll(cpdirtmp, 0777); err != nil {
 		return nil, errors.Wrap(err, "create checkpoint dir")
 	}