diff --git a/server/src/internalClusterTest/java/org/opensearch/remotestore/AbstractRemoteStoreMockRepositoryIntegTestCase.java b/server/src/internalClusterTest/java/org/opensearch/remotestore/AbstractRemoteStoreMockRepositoryIntegTestCase.java
index 5a3e58690b639..9d4d8aa24bd51 100644
--- a/server/src/internalClusterTest/java/org/opensearch/remotestore/AbstractRemoteStoreMockRepositoryIntegTestCase.java
+++ b/server/src/internalClusterTest/java/org/opensearch/remotestore/AbstractRemoteStoreMockRepositoryIntegTestCase.java
@@ -33,7 +33,6 @@
 import static org.opensearch.node.remotestore.RemoteStoreNodeAttribute.REMOTE_STORE_REPOSITORY_TYPE_ATTRIBUTE_KEY_FORMAT;
 import static org.opensearch.node.remotestore.RemoteStoreNodeAttribute.REMOTE_STORE_SEGMENT_REPOSITORY_NAME_ATTRIBUTE_KEY;
 import static org.opensearch.node.remotestore.RemoteStoreNodeAttribute.REMOTE_STORE_TRANSLOG_REPOSITORY_NAME_ATTRIBUTE_KEY;
-import static org.opensearch.test.hamcrest.OpenSearchAssertions.assertAcked;
 
 public abstract class AbstractRemoteStoreMockRepositoryIntegTestCase extends AbstractSnapshotIntegTestCase {
 
@@ -107,13 +106,11 @@ public Settings buildRemoteStoreNodeAttributes(Path repoLocation, double ioFailu
             .build();
     }
 
-    protected void deleteRepo() {
-        logger.info("--> Deleting all the indices");
-        internalCluster().wipeIndices("_all");
-        logger.info("--> Deleting the repository={}", REPOSITORY_NAME);
-        assertAcked(clusterAdmin().prepareDeleteRepository(REPOSITORY_NAME));
-        logger.info("--> Deleting the repository={}", TRANSLOG_REPOSITORY_NAME);
-        assertAcked(clusterAdmin().prepareDeleteRepository(TRANSLOG_REPOSITORY_NAME));
+    protected void cleanupRepo() {
+        logger.info("--> Cleanup the repository={}", REPOSITORY_NAME);
+        clusterAdmin().prepareCleanupRepository(REPOSITORY_NAME).execute().actionGet();
+        logger.info("--> Cleanup the repository={}", TRANSLOG_REPOSITORY_NAME);
+        clusterAdmin().prepareCleanupRepository(TRANSLOG_REPOSITORY_NAME).execute().actionGet();
     }
 
     protected String setup(Path repoLocation, double ioFailureRate, String skipExceptionBlobList, long maxFailure) {
@@ -127,6 +124,8 @@ protected String setup(Path repoLocation, double ioFailureRate, String skipExcep
             settings.put(CLUSTER_REPLICATION_TYPE_SETTING.getKey(), ReplicationType.SEGMENT);
         }
 
+        disableRepoConsistencyCheck("Remote Store Creates System Repository");
+
         internalCluster().startClusterManagerOnlyNode(settings.build());
         String dataNodeName = internalCluster().startDataOnlyNode(settings.build());
         createIndex(INDEX_NAME);
diff --git a/server/src/internalClusterTest/java/org/opensearch/remotestore/RemoteStoreBackpressureIT.java b/server/src/internalClusterTest/java/org/opensearch/remotestore/RemoteStoreBackpressureIT.java
index d02c5bf54fbed..3462054c23630 100644
--- a/server/src/internalClusterTest/java/org/opensearch/remotestore/RemoteStoreBackpressureIT.java
+++ b/server/src/internalClusterTest/java/org/opensearch/remotestore/RemoteStoreBackpressureIT.java
@@ -112,7 +112,7 @@ private void validateBackpressure(
         stats = stats();
         indexDocAndRefresh(initialSource, initialDocsToIndex);
         assertEquals(rejectionCount, stats.rejectionCount);
-        deleteRepo();
+        cleanupRepo();
     }
 
     private RemoteSegmentTransferTracker.Stats stats() {
diff --git a/server/src/internalClusterTest/java/org/opensearch/remotestore/RemoteStoreRefreshListenerIT.java b/server/src/internalClusterTest/java/org/opensearch/remotestore/RemoteStoreRefreshListenerIT.java
index b97e93f323fb2..88760b7bbfad2 100644
--- a/server/src/internalClusterTest/java/org/opensearch/remotestore/RemoteStoreRefreshListenerIT.java
+++ b/server/src/internalClusterTest/java/org/opensearch/remotestore/RemoteStoreRefreshListenerIT.java
@@ -56,7 +56,7 @@ public void testRemoteRefreshRetryOnFailure() throws Exception {
             logger.info("Local files = {}, Repo files = {}", sortedFilesInLocal, sortedFilesInRepo);
             assertTrue(filesInRepo.containsAll(filesInLocal));
         }, 90, TimeUnit.SECONDS);
-        deleteRepo();
+        cleanupRepo();
     }
 
     public void testRemoteRefreshSegmentPressureSettingChanged() {