diff --git a/server/src/internalClusterTest/java/org/opensearch/remotestore/RemoteStorePinnedTimestampsGarbageCollectionIT.java b/server/src/internalClusterTest/java/org/opensearch/remotestore/RemoteStorePinnedTimestampsGarbageCollectionIT.java
index 08ece7df457cc..2922ad33586d2 100644
--- a/server/src/internalClusterTest/java/org/opensearch/remotestore/RemoteStorePinnedTimestampsGarbageCollectionIT.java
+++ b/server/src/internalClusterTest/java/org/opensearch/remotestore/RemoteStorePinnedTimestampsGarbageCollectionIT.java
@@ -421,8 +421,8 @@ public void testIndexDeletionNoPinnedTimestamps() throws Exception {
         client().admin().indices().prepareDelete(INDEX_NAME).get();
 
         assertBusy(() -> {
-            assertEquals(0, Files.list(translogMetadataPath).collect(Collectors.toList()).size());
-            assertEquals(0, Files.list(translogDataPath).collect(Collectors.toList()).size());
+            assertEquals(1, Files.list(translogMetadataPath).collect(Collectors.toList()).size());
+            assertEquals(4, Files.list(translogDataPath).collect(Collectors.toList()).size());
         });
     }
 
@@ -490,7 +490,7 @@ public void testIndexDeletionWithPinnedTimestamps() throws Exception {
 
         assertBusy(() -> {
             List<Path> metadataFiles = Files.list(translogMetadataPath).collect(Collectors.toList());
-            assertEquals(1, metadataFiles.size());
+            assertEquals(2, metadataFiles.size());
 
             verifyTranslogDataFileCount(metadataFiles, translogDataPath);
         });
diff --git a/server/src/internalClusterTest/java/org/opensearch/remotestore/RestoreShallowSnapshotV2IT.java b/server/src/internalClusterTest/java/org/opensearch/remotestore/RestoreShallowSnapshotV2IT.java
index 460d7947ee427..d532abaa2b0ad 100644
--- a/server/src/internalClusterTest/java/org/opensearch/remotestore/RestoreShallowSnapshotV2IT.java
+++ b/server/src/internalClusterTest/java/org/opensearch/remotestore/RestoreShallowSnapshotV2IT.java
@@ -946,9 +946,9 @@ public void testContinuousIndexing() throws Exception {
 
         logger.info("Snapshots Status: " + snapshots);
 
-        for (String snapshot: snapshots.keySet()) {
+        for (String snapshot : snapshots.keySet()) {
             logger.info("Restoring snapshot: {}", snapshot);
-            assertAcked(client().admin().indices().prepareClose(index));
+            assertAcked(client().admin().indices().delete(new DeleteIndexRequest(index)).get());
 
             RestoreSnapshotResponse restoreSnapshotResponse1 = client.admin()
                 .cluster()
diff --git a/server/src/main/java/org/opensearch/index/store/RemoteSegmentStoreDirectory.java b/server/src/main/java/org/opensearch/index/store/RemoteSegmentStoreDirectory.java
index 6559f46bfc868..27a78dc3ce2f6 100644
--- a/server/src/main/java/org/opensearch/index/store/RemoteSegmentStoreDirectory.java
+++ b/server/src/main/java/org/opensearch/index/store/RemoteSegmentStoreDirectory.java
@@ -39,6 +39,7 @@
 import org.opensearch.index.store.lockmanager.RemoteStoreMetadataLockManager;
 import org.opensearch.index.store.remote.metadata.RemoteSegmentMetadata;
 import org.opensearch.index.store.remote.metadata.RemoteSegmentMetadataHandler;
+import org.opensearch.indices.RemoteStoreSettings;
 import org.opensearch.indices.replication.checkpoint.ReplicationCheckpoint;
 import org.opensearch.node.remotestore.RemoteStorePinnedTimestampService;
 import org.opensearch.threadpool.ThreadPool;
@@ -896,6 +897,11 @@ public void deleteStaleSegments(int lastNMetadataFilesToKeep) throws IOException
             return;
         }
 
+        // If pinned timestamps are enabled, make sure to not delete last metadata file.
+        if (RemoteStoreSettings.isPinnedTimestampsEnabled()) {
+            metadataFilesEligibleToDelete.remove(sortedMetadataFileList.get(0));
+        }
+
         List<String> metadataFilesToBeDeleted = metadataFilesEligibleToDelete.stream()
             .filter(metadataFile -> allLockFiles.contains(metadataFile) == false)
             .collect(Collectors.toList());
diff --git a/server/src/main/java/org/opensearch/index/translog/RemoteFsTimestampAwareTranslog.java b/server/src/main/java/org/opensearch/index/translog/RemoteFsTimestampAwareTranslog.java
index 3ccacde22bbfc..ce08f81689b4f 100644
--- a/server/src/main/java/org/opensearch/index/translog/RemoteFsTimestampAwareTranslog.java
+++ b/server/src/main/java/org/opensearch/index/translog/RemoteFsTimestampAwareTranslog.java
@@ -189,7 +189,7 @@ public void onResponse(List<BlobMetadata> blobMetadata) {
                     List<String> metadataFilesToBeDeleted = getMetadataFilesToBeDeleted(metadataFiles, indexDeleted);
 
                     // If index is not deleted, make sure to keep latest metadata file
-                    if (indexDeleted == false) {
+                    if (indexDeleted == false || RemoteStoreSettings.isPinnedTimestampsEnabled()) {
                         metadataFilesToBeDeleted.remove(metadataFiles.get(0));
                     }
 
diff --git a/server/src/test/java/org/opensearch/index/translog/RemoteFsTimestampAwareTranslogTests.java b/server/src/test/java/org/opensearch/index/translog/RemoteFsTimestampAwareTranslogTests.java
index 73db3314f4d1e..01da1774f6800 100644
--- a/server/src/test/java/org/opensearch/index/translog/RemoteFsTimestampAwareTranslogTests.java
+++ b/server/src/test/java/org/opensearch/index/translog/RemoteFsTimestampAwareTranslogTests.java
@@ -285,9 +285,9 @@ public void testIndexDeletionWithNoPinnedTimestampNoRecentMdFiles() throws Excep
         assertBusy(() -> assertTrue(translog.isRemoteGenerationDeletionPermitsAvailable()));
 
         assertBusy(() -> {
-            assertEquals(0, blobStoreTransferService.listAll(getTranslogDirectory().add(METADATA_DIR)).size());
+            assertEquals(1, blobStoreTransferService.listAll(getTranslogDirectory().add(METADATA_DIR)).size());
             assertEquals(
-                0,
+                12,
                 blobStoreTransferService.listAll(getTranslogDirectory().add(DATA_DIR).add(String.valueOf(primaryTerm.get()))).size()
             );
         });