diff --git a/server/src/test/java/org/opensearch/index/shard/IndexShardTests.java b/server/src/test/java/org/opensearch/index/shard/IndexShardTests.java
index e5bfa8caee79a..3188de13bb00b 100644
--- a/server/src/test/java/org/opensearch/index/shard/IndexShardTests.java
+++ b/server/src/test/java/org/opensearch/index/shard/IndexShardTests.java
@@ -2956,6 +2956,14 @@ public void testRestoreShardFromRemoteStore(boolean performFlush) throws IOExcep
             )
         );
 
+        // Make sure to drain refreshes from the shard. Otherwise, if the refresh is in-progress, it overlaps with
+        // deletion of segment files in the subsequent code block.
+        for (ReferenceManager.RefreshListener refreshListener : target.getEngine().config().getInternalRefreshListener()) {
+            if (refreshListener instanceof ReleasableRetryableRefreshListener) {
+                ((ReleasableRetryableRefreshListener) refreshListener).drainRefreshes();
+            }
+        }
+
         // Delete files in store directory to restore from remote directory
         Directory storeDirectory = target.store().directory();