diff --git a/pkg/storage/stores/shipper/indexshipper/tsdb/compactor.go b/pkg/storage/stores/shipper/indexshipper/tsdb/compactor.go
index 06028ce1d63d2..ee9784a02db8e 100644
--- a/pkg/storage/stores/shipper/indexshipper/tsdb/compactor.go
+++ b/pkg/storage/stores/shipper/indexshipper/tsdb/compactor.go
@@ -269,7 +269,7 @@ type compactedIndex struct {
 	tableInterval model.Interval
 	periodConfig  config.PeriodConfig
 
-	indexChunks     []chunk.Chunk
+	indexChunks     map[string][]tsdbindex.ChunkMeta
 	deleteChunks    map[string][]tsdbindex.ChunkMeta
 	seriesToCleanup map[string]struct{}
 }
@@ -282,6 +282,7 @@ func newCompactedIndex(ctx context.Context, tableName, userID, workingDir string
 		workingDir:      workingDir,
 		periodConfig:    periodConfig,
 		tableInterval:   retention.ExtractIntervalFromTableName(tableName),
+		indexChunks:     map[string][]tsdbindex.ChunkMeta{},
 		deleteChunks:    map[string][]tsdbindex.ChunkMeta{},
 		seriesToCleanup: map[string]struct{}{},
 	}
@@ -338,7 +339,20 @@ func (c *compactedIndex) IndexChunk(chk chunk.Chunk) (bool, error) {
 		return false, nil
 	}
 
-	c.indexChunks = append(c.indexChunks, chk)
+	// TSDB doesnt need the __name__="log" convention the old chunk store index used.
+	b := labels.NewBuilder(chk.Metric)
+	b.Del(labels.MetricName)
+	ls := b.Labels().String()
+
+	approxKB := math.Round(float64(chk.Data.UncompressedSize()) / float64(1<<10))
+
+	c.indexChunks[ls] = append(c.indexChunks[ls], tsdbindex.ChunkMeta{
+		Checksum: chk.Checksum,
+		MinTime:  int64(chk.From),
+		MaxTime:  int64(chk.Through),
+		KB:       uint32(approxKB),
+		Entries:  uint32(chk.Data.Entries()),
+	})
 
 	return true, nil
 }
@@ -372,22 +386,12 @@ func (c *compactedIndex) ToIndexFile() (shipperindex.Index, error) {
 	}
 	c.deleteChunks = nil
 
-	for _, chk := range c.indexChunks {
-		// TSDB doesnt need the __name__="log" convention the old chunk store index used.
-		b := labels.NewBuilder(chk.Metric)
-		b.Del(labels.MetricName)
-		ls := b.Labels()
-
-		approxKB := math.Round(float64(chk.Data.UncompressedSize()) / float64(1<<10))
-		err := c.builder.InsertChunk(ls.String(), tsdbindex.ChunkMeta{
-			Checksum: chk.Checksum,
-			MinTime:  int64(chk.From),
-			MaxTime:  int64(chk.Through),
-			KB:       uint32(approxKB),
-			Entries:  uint32(chk.Data.Entries()),
-		})
-		if err != nil {
-			return nil, err
+	for ls, metas := range c.indexChunks {
+		for i := range metas {
+			err := c.builder.InsertChunk(ls, metas[i])
+			if err != nil {
+				return nil, err
+			}
 		}
 	}
 	c.indexChunks = nil