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 7b57fabdf1486..9c1e902606cab 100644
--- a/server/src/main/java/org/opensearch/index/store/RemoteSegmentStoreDirectory.java
+++ b/server/src/main/java/org/opensearch/index/store/RemoteSegmentStoreDirectory.java
@@ -45,7 +45,6 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.nio.file.NoSuchFileException;
-import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
@@ -781,6 +780,7 @@ public void deleteStaleSegments(int lastNMetadataFilesToKeep) throws IOException
                 segmentMetadataMap.values().stream().map(metadata -> metadata.uploadedFilename).collect(Collectors.toSet())
             );
         }
+        Set<String> deletedSegmentFiles = new HashSet<>();
         for (String metadataFile : metadataFilesToBeDeleted) {
             Map<String, UploadedSegmentMetadata> staleSegmentFilesMetadataMap = readMetadataFile(metadataFile).getMetadata();
             Set<String> staleSegmentRemoteFilenames = staleSegmentFilesMetadataMap.values()
@@ -788,31 +788,33 @@ public void deleteStaleSegments(int lastNMetadataFilesToKeep) throws IOException
                 .map(metadata -> metadata.uploadedFilename)
                 .collect(Collectors.toSet());
             AtomicBoolean deletionSuccessful = new AtomicBoolean(true);
-            List<String> nonActiveDeletedSegmentFiles = new ArrayList<>();
-            staleSegmentRemoteFilenames.stream().filter(file -> !activeSegmentRemoteFilenames.contains(file)).forEach(file -> {
-                try {
-                    remoteDataDirectory.deleteFile(file);
-                    nonActiveDeletedSegmentFiles.add(file);
-                    if (!activeSegmentFilesMetadataMap.containsKey(getLocalSegmentFilename(file))) {
-                        segmentsUploadedToRemoteStore.remove(getLocalSegmentFilename(file));
+            staleSegmentRemoteFilenames.stream()
+                .filter(file -> activeSegmentRemoteFilenames.contains(file) == false)
+                .filter(file -> deletedSegmentFiles.contains(file) == false)
+                .forEach(file -> {
+                    try {
+                        remoteDataDirectory.deleteFile(file);
+                        deletedSegmentFiles.add(file);
+                        if (!activeSegmentFilesMetadataMap.containsKey(getLocalSegmentFilename(file))) {
+                            segmentsUploadedToRemoteStore.remove(getLocalSegmentFilename(file));
+                        }
+                    } catch (NoSuchFileException e) {
+                        logger.info("Segment file {} corresponding to metadata file {} does not exist in remote", file, metadataFile);
+                    } catch (IOException e) {
+                        deletionSuccessful.set(false);
+                        logger.warn(
+                            "Exception while deleting segment file {} corresponding to metadata file {}. Deletion will be re-tried",
+                            file,
+                            metadataFile
+                        );
                     }
-                } catch (NoSuchFileException e) {
-                    logger.info("Segment file {} corresponding to metadata file {} does not exist in remote", file, metadataFile);
-                } catch (IOException e) {
-                    deletionSuccessful.set(false);
-                    logger.info(
-                        "Exception while deleting segment file {} corresponding to metadata file {}. Deletion will be re-tried",
-                        file,
-                        metadataFile
-                    );
-                }
-            });
-            logger.debug("nonActiveDeletedSegmentFiles={}", nonActiveDeletedSegmentFiles);
+                });
             if (deletionSuccessful.get()) {
                 logger.debug("Deleting stale metadata file {} from remote segment store", metadataFile);
                 remoteMetadataDirectory.deleteFile(metadataFile);
             }
         }
+        logger.debug("deletedSegmentFiles={}", deletedSegmentFiles);
     }
 
     public void deleteStaleSegmentsAsync(int lastNMetadataFilesToKeep) {
diff --git a/server/src/test/java/org/opensearch/index/store/RemoteSegmentStoreDirectoryTests.java b/server/src/test/java/org/opensearch/index/store/RemoteSegmentStoreDirectoryTests.java
index 36cfd84ff960a..2c6c4afed69fd 100644
--- a/server/src/test/java/org/opensearch/index/store/RemoteSegmentStoreDirectoryTests.java
+++ b/server/src/test/java/org/opensearch/index/store/RemoteSegmentStoreDirectoryTests.java
@@ -51,6 +51,7 @@
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -122,6 +123,14 @@ public class RemoteSegmentStoreDirectoryTests extends IndexShardTestCase {
         1,
         "node-1"
     );
+    private final String metadataFilename4 = RemoteSegmentStoreDirectory.MetadataFilenameUtils.getMetadataFilename(
+        10,
+        36,
+        34,
+        1,
+        1,
+        "node-1"
+    );
 
     @Before
     public void setup() throws IOException {
@@ -979,6 +988,51 @@ public void testDeleteStaleCommitsActualDelete() throws Exception {
         verify(remoteMetadataDirectory).deleteFile(metadataFilename3);
     }
 
+    public void testDeleteStaleCommitsDeleteDedup() throws Exception {
+        Map<String, Map<String, String>> metadataFilenameContentMapping = new HashMap<>(populateMetadata());
+        metadataFilenameContentMapping.put(metadataFilename4, metadataFilenameContentMapping.get(metadataFilename3));
+
+        when(
+            remoteMetadataDirectory.listFilesByPrefixInLexicographicOrder(
+                RemoteSegmentStoreDirectory.MetadataFilenameUtils.METADATA_PREFIX,
+                Integer.MAX_VALUE
+            )
+        ).thenReturn(new ArrayList<>(List.of(metadataFilename, metadataFilename2, metadataFilename3, metadataFilename4)));
+
+        when(remoteMetadataDirectory.getBlobStream(metadataFilename4)).thenAnswer(
+            I -> createMetadataFileBytes(
+                metadataFilenameContentMapping.get(metadataFilename4),
+                indexShard.getLatestReplicationCheckpoint(),
+                segmentInfos
+            )
+        );
+
+        remoteSegmentStoreDirectory.init();
+
+        // popluateMetadata() adds stub to return 4 metadata files
+        // We are passing lastNMetadataFilesToKeep=2 here so that oldest 2 metadata files will be deleted
+        remoteSegmentStoreDirectory.deleteStaleSegmentsAsync(2);
+
+        Set<String> staleSegmentFiles = new HashSet<>();
+        for (String metadata : metadataFilenameContentMapping.get(metadataFilename3).values()) {
+            staleSegmentFiles.add(metadata.split(RemoteSegmentStoreDirectory.UploadedSegmentMetadata.SEPARATOR)[1]);
+        }
+        for (String metadata : metadataFilenameContentMapping.get(metadataFilename4).values()) {
+            staleSegmentFiles.add(metadata.split(RemoteSegmentStoreDirectory.UploadedSegmentMetadata.SEPARATOR)[1]);
+        }
+        staleSegmentFiles.forEach(file -> {
+            try {
+                // Even with the same files in 2 stale metadata files, delete should be called only once.
+                verify(remoteDataDirectory, times(1)).deleteFile(file);
+            } catch (IOException e) {
+                throw new RuntimeException(e);
+            }
+        });
+        assertBusy(() -> assertThat(remoteSegmentStoreDirectory.canDeleteStaleCommits.get(), is(true)));
+        verify(remoteMetadataDirectory).deleteFile(metadataFilename3);
+        verify(remoteMetadataDirectory).deleteFile(metadataFilename4);
+    }
+
     public void testDeleteStaleCommitsActualDeleteIOException() throws Exception {
         Map<String, Map<String, String>> metadataFilenameContentMapping = populateMetadata();
         remoteSegmentStoreDirectory.init();