diff --git a/pkg/block/indexheader/binary_reader.go b/pkg/block/indexheader/binary_reader.go
index 9005cd443b..e14e98be3f 100644
--- a/pkg/block/indexheader/binary_reader.go
+++ b/pkg/block/indexheader/binary_reader.go
@@ -71,20 +71,21 @@ type BinaryTOC struct {
 }
 
 // WriteBinary build index-header file from the pieces of index in object storage.
-func WriteBinary(ctx context.Context, bkt objstore.BucketReader, id ulid.ULID, fn string) (err error) {
+func WriteBinary(ctx context.Context, bkt objstore.BucketReader, id ulid.ULID, filename string) (err error) {
 	ir, indexVersion, err := newChunkedIndexReader(ctx, bkt, id)
 	if err != nil {
 		return errors.Wrap(err, "new index reader")
 	}
+	tmpFilename := filename + ".tmp"
 
 	// Buffer for copying and encbuffers.
 	// This also will control the size of file writer buffer.
 	buf := make([]byte, 32*1024)
-	bw, err := newBinaryWriter(fn, buf)
+	bw, err := newBinaryWriter(tmpFilename, buf)
 	if err != nil {
 		return errors.Wrap(err, "new binary index header writer")
 	}
-	defer runutil.CloseWithErrCapture(&err, bw, "close binary writer for %s", fn)
+	defer runutil.CloseWithErrCapture(&err, bw, "close binary writer for %s", tmpFilename)
 
 	if err := bw.AddIndexMeta(indexVersion, ir.toc.PostingsTable); err != nil {
 		return errors.Wrap(err, "add index meta")
@@ -109,7 +110,17 @@ func WriteBinary(ctx context.Context, bkt objstore.BucketReader, id ulid.ULID, f
 	if err := bw.WriteTOC(); err != nil {
 		return errors.Wrap(err, "write index header TOC")
 	}
-	return nil
+
+	if err := bw.f.Flush(); err != nil {
+		return errors.Wrap(err, "flush")
+	}
+
+	if err := bw.f.f.Sync(); err != nil {
+		return errors.Wrap(err, "sync")
+	}
+
+	// Create index-header in atomic way, to avoid partial writes (e.g during restart or crash of store GW).
+	return os.Rename(tmpFilename, filename)
 }
 
 type chunkedIndexReader struct {