diff --git a/processing/src/main/java/org/apache/druid/segment/IndexMerger.java b/processing/src/main/java/org/apache/druid/segment/IndexMerger.java
index 4661b652eeda..a961a8143a08 100644
--- a/processing/src/main/java/org/apache/druid/segment/IndexMerger.java
+++ b/processing/src/main/java/org/apache/druid/segment/IndexMerger.java
@@ -189,6 +189,15 @@ File persist(
       @Nullable SegmentWriteOutMediumFactory segmentWriteOutMediumFactory
   ) throws IOException;
 
+  File mergeSegmentFiles(
+      File[] segmentFiles,
+      boolean rollup,
+      AggregatorFactory[] metricAggs,
+      File outDir,
+      IndexSpec indexSpec,
+      @Nullable SegmentWriteOutMediumFactory segmentWriteOutMediumFactory
+  ) throws IOException;
+
   File mergeQueryableIndex(
       List<QueryableIndex> indexes,
       boolean rollup,
diff --git a/processing/src/main/java/org/apache/druid/segment/IndexMergerV9.java b/processing/src/main/java/org/apache/druid/segment/IndexMergerV9.java
index 135f8cb1266d..850b10ca0112 100644
--- a/processing/src/main/java/org/apache/druid/segment/IndexMergerV9.java
+++ b/processing/src/main/java/org/apache/druid/segment/IndexMergerV9.java
@@ -798,6 +798,40 @@ public File persist(
     );
   }
 
+  @Override
+  public File mergeSegmentFiles(
+      File[] segmentFiles,
+      boolean rollup,
+      AggregatorFactory[] metricAggs,
+      File outDir,
+      IndexSpec indexSpec,
+      @Nullable SegmentWriteOutMediumFactory segmentWriteOutMediumFactory
+  ) throws IOException
+  {
+    List<QueryableIndex> indexes = Lists.transform(Arrays.asList(segmentFiles), input -> {
+      try {
+        return indexIO.loadIndex(input);
+      }
+      catch (IOException e) {
+        throw new ISE(e, "load index %s failed!?", input.getAbsolutePath());
+      }
+    });
+
+    try {
+      return mergeQueryableIndex(indexes, rollup, metricAggs, outDir, indexSpec, new BaseProgressIndicator(), segmentWriteOutMediumFactory);
+    }
+    finally {
+      for (QueryableIndex index : indexes) {
+        try {
+          index.close();
+        }
+        catch (Exception e) {
+          log.warn(e, "failed to close index when merge");
+        }
+      }
+    }
+  }
+
   @Override
   public File mergeQueryableIndex(
       List<QueryableIndex> indexes,
diff --git a/server/src/main/java/org/apache/druid/segment/realtime/appenderator/AppenderatorImpl.java b/server/src/main/java/org/apache/druid/segment/realtime/appenderator/AppenderatorImpl.java
index 9c837b088161..8df64bfd388d 100644
--- a/server/src/main/java/org/apache/druid/segment/realtime/appenderator/AppenderatorImpl.java
+++ b/server/src/main/java/org/apache/druid/segment/realtime/appenderator/AppenderatorImpl.java
@@ -82,6 +82,7 @@
 import javax.annotation.Nullable;
 import java.io.Closeable;
 import java.io.File;
+import java.io.FilenameFilter;
 import java.io.IOException;
 import java.nio.channels.FileChannel;
 import java.nio.channels.FileLock;
@@ -716,8 +717,20 @@ private DataSegment mergeAndPush(final SegmentIdentifier identifier, final Sink
           closer.register(segmentAndCloseable.rhs);
         }
 
-        mergedFile = indexMerger.mergeQueryableIndex(
-            indexes,
+        File[] hydrantDirs = persistDir.listFiles(
+            new FilenameFilter()
+            {
+              @Override
+              public boolean accept(File dir, String fileName)
+              {
+                // To avoid reading and listing of "merged" dir
+                return !(Ints.tryParse(fileName) == null);
+              }
+            }
+        );
+
+        mergedFile = indexMerger.mergeSegmentFiles(
+            hydrantDirs,
             schema.getGranularitySpec().isRollup(),
             schema.getAggregators(),
             mergedTarget,
diff --git a/server/src/main/java/org/apache/druid/segment/realtime/plumber/RealtimePlumber.java b/server/src/main/java/org/apache/druid/segment/realtime/plumber/RealtimePlumber.java
index b0453d90c388..d8eed2d3ba2e 100644
--- a/server/src/main/java/org/apache/druid/segment/realtime/plumber/RealtimePlumber.java
+++ b/server/src/main/java/org/apache/druid/segment/realtime/plumber/RealtimePlumber.java
@@ -430,8 +430,20 @@ public void doRun()
                   closer.register(segmentAndCloseable.rhs);
                 }
 
-                mergedFile = indexMerger.mergeQueryableIndex(
-                    indexes,
+                File[] hydrantDirs = persistDir.listFiles(
+                    new FilenameFilter()
+                    {
+                      @Override
+                      public boolean accept(File dir, String fileName)
+                      {
+                        // To avoid reading and listing of "merged" dir
+                        return !(Ints.tryParse(fileName) == null);
+                      }
+                    }
+                );
+
+                mergedFile = indexMerger.mergeSegmentFiles(
+                    hydrantDirs,
                     schema.getGranularitySpec().isRollup(),
                     schema.getAggregators(),
                     mergedTarget,