diff --git a/pkg/service/backup/worker_deduplicate.go b/pkg/service/backup/worker_deduplicate.go
index f526f0c75..2b259c052 100644
--- a/pkg/service/backup/worker_deduplicate.go
+++ b/pkg/service/backup/worker_deduplicate.go
@@ -84,17 +84,21 @@ func (w *worker) deduplicateHost(ctx context.Context, h hostInfo) error {
 			}
 		}
 
-		deduplicatedByUUID, err := w.deduplicateUUIDSStables(ctx, d.Path, h.IP, remoteSSTableBundles, localSSTableBundles)
+		deduplicatedUUIDSSTables := w.deduplicateUUIDSStables(remoteSSTableBundles, localSSTableBundles)
+		deduplicatedIntSSTables, err := w.deduplicateIntSSTables(ctx, h.IP, dataDst, d.Path, remoteSSTableBundles, localSSTableBundles)
 		if err != nil {
-			return errors.Wrap(err, "deduplicate based on UUID as generation id content")
+			return errors.Wrap(err, "deduplication based on .crc32 content")
 		}
-		d.Progress.Skipped += deduplicatedByUUID
+		deduplicated := make([]string, 0, len(deduplicatedUUIDSSTables)+len(deduplicatedIntSSTables))
 
-		deduplicatedByCrc32, err := w.deduplicateIntSSTables(ctx, h.IP, dataDst, d.Path, remoteSSTableBundles, localSSTableBundles)
+		for _, fi := range deduplicatedUUIDSSTables {
+			d.Progress.Skipped += fi.Size
+			deduplicated = append(deduplicated, fi.Name)
+		}
+		_, err = w.Client.RcloneDeletePathsInBatches(ctx, h.IP, d.Path, deduplicated, 1000)
 		if err != nil {
-			return errors.Wrap(err, "deduplication based on .crc32 content")
+			return errors.Wrap(err, "delete deduplicated files")
 		}
-		d.Progress.Skipped += deduplicatedByCrc32
 
 		return nil
 	}
@@ -112,11 +116,10 @@ func (w *worker) deduplicateHost(ctx context.Context, h hostInfo) error {
 	return parallel.Run(len(dirs), 1, f, notify)
 }
 
-func (w *worker) deduplicateUUIDSStables(ctx context.Context, host string, snapshotDir string,
-	remoteSSTables, localSSTables *sstableBundlesByID,
-) (deduplicated int64, err error) {
+func (w *worker) deduplicateUUIDSStables(remoteSSTables, localSSTables *sstableBundlesByID) []fileInfo {
 	// SSTable bundle with UUID generation ID can be manually deduplicated
 	// when SSTable bundle with the same UUID is already present on the remote.
+	deduplicated := make([]fileInfo, 0)
 	for id, localBundle := range localSSTables.uuidID {
 		remoteBundle, ok := remoteSSTables.uuidID[id]
 		if !ok {
@@ -125,24 +128,14 @@ func (w *worker) deduplicateUUIDSStables(ctx context.Context, host string, snaps
 		if !isSSTableBundleSizeEqual(localBundle, remoteBundle) {
 			continue
 		}
-		// Remove duplicated SSTable from local snapshot
-		for _, fi := range localBundle {
-			localPath := path.Join(snapshotDir, fi.Name)
-			w.Logger.Debug(ctx, "Removing local snapshot file (deduplication based on generation UUID)",
-				"host", host, "file", localPath)
-			if err := w.Client.RcloneDeleteFile(ctx, host, localPath); err != nil {
-				return deduplicated, errors.Wrapf(err, "delete local snapshot's SSTable file %s", localPath)
-			}
-			deduplicated += fi.Size
-		}
+		deduplicated = append(deduplicated, localBundle...)
 	}
-
-	return deduplicated, nil
+	return deduplicated
 }
 
 func (w *worker) deduplicateIntSSTables(ctx context.Context, host string, remoteDir, localDir string,
 	remoteSSTables, localSSTables *sstableBundlesByID,
-) (deduplicated int64, err error) {
+) (deduplicated []fileInfo, err error) {
 	// Reference to SSTables 3.0 Data File Format
 	// https://opensource.docs.scylladb.com/stable/architecture/sstable/sstable3/sstables-3-data-file-format.html
 
@@ -177,16 +170,8 @@ func (w *worker) deduplicateIntSSTables(ctx context.Context, host string, remote
 			return deduplicated, errors.Wrapf(err, "get content of local CRC32 %s", localCRC32Path)
 		}
 
-		if !bytes.Equal(localCRC32, remoteCRC32) {
-			continue
-		}
-		for _, fi := range localBundle {
-			localPath := path.Join(localDir, fi.Name)
-			w.Logger.Debug(ctx, "Removing local snapshot file (deduplication based on .crc32)", "host", host, "file", localPath)
-			if err := w.Client.RcloneDeleteFile(ctx, host, localPath); err != nil {
-				return deduplicated, errors.Wrapf(err, "delete local snapshot's SSTable file %s", localPath)
-			}
-			deduplicated += fi.Size
+		if bytes.Equal(localCRC32, remoteCRC32) {
+			deduplicated = append(deduplicated, localBundle...)
 		}
 	}
 	return deduplicated, nil