diff --git a/server/src/main/java/org/opensearch/gateway/remote/ClusterMetadataManifest.java b/server/src/main/java/org/opensearch/gateway/remote/ClusterMetadataManifest.java
index bf02c73ca560b..7622b07185f47 100644
--- a/server/src/main/java/org/opensearch/gateway/remote/ClusterMetadataManifest.java
+++ b/server/src/main/java/org/opensearch/gateway/remote/ClusterMetadataManifest.java
@@ -638,6 +638,7 @@ public Builder clusterUUIDCommitted(boolean clusterUUIDCommitted) {
         public Builder() {
             indices = new ArrayList<>();
             customMetadataMap = new HashMap<>();
+            indicesRouting = new ArrayList<>();
         }
 
         public Builder(ClusterMetadataManifest manifest) {
diff --git a/server/src/main/java/org/opensearch/gateway/remote/RemoteClusterStateCleanupManager.java b/server/src/main/java/org/opensearch/gateway/remote/RemoteClusterStateCleanupManager.java
index 8a106a25e5630..547a40120883a 100644
--- a/server/src/main/java/org/opensearch/gateway/remote/RemoteClusterStateCleanupManager.java
+++ b/server/src/main/java/org/opensearch/gateway/remote/RemoteClusterStateCleanupManager.java
@@ -24,9 +24,11 @@
 import org.opensearch.core.action.ActionListener;
 import org.opensearch.index.translog.transfer.BlobStoreTransferService;
 import org.opensearch.threadpool.ThreadPool;
+import org.opensearch.cluster.routing.remote.RemoteRoutingTableService;
 
 import java.io.Closeable;
 import java.io.IOException;
+import java.sql.Blob;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
@@ -171,6 +173,7 @@ void deleteClusterMetadata(
             Set<String> staleManifestPaths = new HashSet<>();
             Set<String> staleIndexMetadataPaths = new HashSet<>();
             Set<String> staleGlobalMetadataPaths = new HashSet<>();
+            Set<String> staleIndexRoutingPaths = new HashSet<>();
             activeManifestBlobMetadata.forEach(blobMetadata -> {
                 ClusterMetadataManifest clusterMetadataManifest = remoteClusterStateService.fetchRemoteClusterMetadataManifest(
                     clusterName,
@@ -189,6 +192,10 @@ void deleteClusterMetadata(
                         .values()
                         .forEach(attribute -> filesToKeep.add(attribute.getUploadedFilename()));
                 }
+                if (clusterMetadataManifest.getCodecVersion() >= ClusterMetadataManifest.CODEC_V3) {
+                    clusterMetadataManifest.getIndicesRouting()
+                        .forEach(uploadedIndicesRouting -> filesToKeep.add(uploadedIndicesRouting.getUploadedFilename()));
+                }
             });
             staleManifestBlobMetadata.forEach(blobMetadata -> {
                 ClusterMetadataManifest clusterMetadataManifest = remoteClusterStateService.fetchRemoteClusterMetadataManifest(
@@ -221,6 +228,14 @@ void deleteClusterMetadata(
                             attribute -> addStaleGlobalMetadataPath(attribute.getUploadedFilename(), filesToKeep, staleGlobalMetadataPaths)
                         );
                 }
+                if (clusterMetadataManifest.getCodecVersion() >= ClusterMetadataManifest.CODEC_V3) {
+                    clusterMetadataManifest.getIndicesRouting().forEach(uploadedIndicesRouting -> {
+                        if (filesToKeep.contains(uploadedIndicesRouting.getUploadedFilename()) == false){
+                            staleIndexRoutingPaths.add(new BlobPath().buildAsString() + uploadedIndicesRouting.getUploadedFilename());
+                            logger.debug("Indices routing paths in stale manifest: {}", uploadedIndicesRouting.getUploadedFilename());
+                        }
+                    });
+                }
 
                 clusterMetadataManifest.getIndices().forEach(uploadedIndexMetadata -> {
                     if (filesToKeep.contains(uploadedIndexMetadata.getUploadedFilename()) == false) {
@@ -240,6 +255,7 @@ void deleteClusterMetadata(
             deleteStalePaths(clusterName, clusterUUID, new ArrayList<>(staleGlobalMetadataPaths));
             deleteStalePaths(clusterName, clusterUUID, new ArrayList<>(staleIndexMetadataPaths));
             deleteStalePaths(clusterName, clusterUUID, new ArrayList<>(staleManifestPaths));
+            deleteStaleIndexRoutingPaths(new ArrayList<>(staleIndexRoutingPaths));
         } catch (IllegalStateException e) {
             logger.error("Error while fetching Remote Cluster Metadata manifests", e);
         } catch (IOException e) {
@@ -344,6 +360,14 @@ void deleteStalePaths(String clusterName, String clusterUUID, List<String> stale
         );
     }
 
+    void deleteStaleIndexRoutingPaths(List<String> stalePaths) throws IOException {
+        logger.debug(String.format(Locale.ROOT, "Deleting stale index routing files from remote - %s", stalePaths));
+        getBlobStoreTransferService().deleteBlobs(
+            BlobPath.cleanPath(),
+            stalePaths
+        );
+    }
+
     /**
      * Purges all remote cluster state against provided cluster UUIDs
      * @param clusterState current state of the cluster
diff --git a/server/src/test/java/org/opensearch/gateway/remote/RemoteClusterStateCleanupManagerTests.java b/server/src/test/java/org/opensearch/gateway/remote/RemoteClusterStateCleanupManagerTests.java
index 24fd1b164a4ff..a547ffb1ee591 100644
--- a/server/src/test/java/org/opensearch/gateway/remote/RemoteClusterStateCleanupManagerTests.java
+++ b/server/src/test/java/org/opensearch/gateway/remote/RemoteClusterStateCleanupManagerTests.java
@@ -155,11 +155,13 @@ public void testDeleteClusterMetadata() throws IOException {
         List<BlobMetadata> inactiveBlobs = Arrays.asList(
             new PlainBlobMetadata("manifest1.dat", 1L),
             new PlainBlobMetadata("manifest2.dat", 1L),
-            new PlainBlobMetadata("manifest3.dat", 1L)
+            new PlainBlobMetadata("manifest3.dat", 1L),
+            new PlainBlobMetadata("manifest6.dat", 1L)
         );
         List<BlobMetadata> activeBlobs = Arrays.asList(
             new PlainBlobMetadata("manifest4.dat", 1L),
-            new PlainBlobMetadata("manifest5.dat", 1L)
+            new PlainBlobMetadata("manifest5.dat", 1L),
+            new PlainBlobMetadata("manifest7.dat", 1L)
         );
         UploadedIndexMetadata index1Metadata = new UploadedIndexMetadata("index1", "indexUUID1", "index_metadata1");
         UploadedIndexMetadata index2Metadata = new UploadedIndexMetadata("index2", "indexUUID2", "index_metadata2");
@@ -199,6 +201,39 @@ public void testDeleteClusterMetadata() throws IOException {
             .settingMetadata(settingMetadataUpdated)
             .build();
 
+        List<UploadedIndexMetadata> indicesRouting1 = List.of(index1Metadata, index2Metadata);
+        List<UploadedIndexMetadata> indicesRouting2 = List.of(index1Metadata);
+        ClusterMetadataManifest manifest6 = ClusterMetadataManifest.builder()
+            .indices(List.of(index1UpdatedMetadata))
+            .globalMetadataFileName("global_metadata")
+            .clusterTerm(1L)
+            .stateVersion(1L)
+            .codecVersion(CODEC_V3)
+            .stateUUID(randomAlphaOfLength(10))
+            .clusterUUID(clusterUUID)
+            .nodeId("nodeA")
+            .opensearchVersion(VersionUtils.randomOpenSearchVersion(random()))
+            .previousClusterUUID(ClusterState.UNKNOWN_UUID)
+            .committed(true)
+            .routingTableVersion(0L)
+            .indicesRouting(indicesRouting1)
+            .build();
+        ClusterMetadataManifest manifest7 = ClusterMetadataManifest.builder()
+            .indices(List.of(index1UpdatedMetadata))
+            .globalMetadataFileName("global_metadata")
+            .clusterTerm(1L)
+            .stateVersion(1L)
+            .codecVersion(CODEC_V3)
+            .stateUUID(randomAlphaOfLength(10))
+            .clusterUUID(clusterUUID)
+            .nodeId("nodeA")
+            .opensearchVersion(VersionUtils.randomOpenSearchVersion(random()))
+            .previousClusterUUID(ClusterState.UNKNOWN_UUID)
+            .committed(true)
+            .routingTableVersion(0L)
+            .indicesRouting(indicesRouting2)
+            .build();
+
         // active manifest have reference to index1Updated, index2, settingsUpdated, coordinationUpdated, templates, templatesUpdated
         ClusterMetadataManifest manifest4 = ClusterMetadataManifest.builder(manifest3)
             .coordinationMetadata(coordinationMetadataUpdated)
@@ -210,8 +245,11 @@ public void testDeleteClusterMetadata() throws IOException {
             manifest5,
             manifest1,
             manifest2,
-            manifest3
+            manifest3,
+            manifest6,
+            manifest7
         );
+
         BlobContainer container = mock(BlobContainer.class);
         when(blobStore.blobContainer(any())).thenReturn(container);
         doNothing().when(container).deleteBlobsIgnoringIfNotExists(any());
@@ -231,6 +269,7 @@ public void testDeleteClusterMetadata() throws IOException {
                     + ".dat"
             )
         );
+        verify(container).deleteBlobsIgnoringIfNotExists(List.of(new BlobPath().buildAsString() + index1Metadata.getUploadedFilename()));
         Set<String> staleManifest = new HashSet<>();
         inactiveBlobs.forEach(blob -> staleManifest.add(new BlobPath().add(MANIFEST_PATH_TOKEN).buildAsString() + blob.name()));
         verify(container).deleteBlobsIgnoringIfNotExists(new ArrayList<>(staleManifest));