diff --git a/server/src/main/java/org/opensearch/index/store/Store.java b/server/src/main/java/org/opensearch/index/store/Store.java
index 62bb6050900df..e9c05768bc509 100644
--- a/server/src/main/java/org/opensearch/index/store/Store.java
+++ b/server/src/main/java/org/opensearch/index/store/Store.java
@@ -821,17 +821,14 @@ public void cleanupAndPreserveLatestCommitPoint(String reason, SegmentInfos info
      *
      * @throws IllegalStateException if the latest snapshot in this store differs from the given one after the cleanup.
      */
-    public void cleanupAndPreserveLatestCommitPoint(
-        String reason,
-        SegmentInfos infos,
-        SegmentInfos lastCommittedSegmentInfos
-    ) throws IOException {
+    public void cleanupAndPreserveLatestCommitPoint(String reason, SegmentInfos infos, SegmentInfos lastCommittedSegmentInfos)
+        throws IOException {
         assert indexSettings.isSegRepEnabled();
         // fetch a snapshot from the latest on disk Segments_N file. This can be behind
         // the passed in local in memory snapshot, so we want to ensure files it references are not removed.
         metadataLock.writeLock().lock();
         try (Lock writeLock = directory.obtainLock(IndexWriter.WRITE_LOCK_NAME)) {
-            cleanupFiles(reason, lastCommittedSegmentInfos.files(true), infos.files(true));
+            cleanupFiles(List.of(directory.listAll()), reason, lastCommittedSegmentInfos.files(true), infos.files(true));
         } finally {
             metadataLock.writeLock().unlock();
         }
@@ -843,31 +840,34 @@ public void cleanupAndPreserveLatestCommitPoint(
      * Performs cleanup of un-referenced files intended to be used after reader close action
      *
      * @param reason Reason for cleanup
-     * @param filesToConsider Files to consider for clean up
+     * @param filesToCleanUp Files to consider for clean up
      * @throws IOException Exception from cleanup operation
      */
-    public void cleanupUnReferencedFiles(String reason, Collection<String> filesToConsider) throws IOException {
+    public void cleanupUnReferencedFiles(String reason, Collection<String> filesToCleanUp) throws IOException {
         assert indexSettings.isSegRepEnabled();
         metadataLock.writeLock().lock();
         try (Lock writeLock = directory.obtainLock(IndexWriter.WRITE_LOCK_NAME)) {
-            cleanupFiles(reason, null, filesToConsider);
+            cleanupFiles(filesToCleanUp, reason, null, null);
         } finally {
             metadataLock.writeLock().unlock();
         }
     }
 
     private void cleanupFiles(
+        Collection<String> filesToCleanUp,
         String reason,
         Collection<String> localSnapshot,
         @Nullable Collection<String> additionalFiles
     ) throws IOException {
         assert metadataLock.isWriteLockedByCurrentThread();
-        for (String existingFile : directory.listAll()) {
+        for (String existingFile : filesToCleanUp) {
             if (Store.isAutogenerated(existingFile)
                 || localSnapshot != null && localSnapshot.contains(existingFile)
                 || (additionalFiles != null && additionalFiles.contains(existingFile))
                 // also ensure we are not deleting a file referenced by an active reader.
-                || replicaFileTracker != null && replicaFileTracker.canDelete(existingFile) == false) {
+                || replicaFileTracker != null && replicaFileTracker.canDelete(existingFile) == false
+                // Prevent temporary replication files as it should be cleaned up MultiFileWriter
+                || existingFile.startsWith(REPLICATION_PREFIX)) {
                 // don't delete snapshot file, or the checksums file (note, this is extra protection since the Store won't delete
                 // checksum)
                 continue;