diff --git a/server/src/test/java/org/elasticsearch/index/shard/IndexShardIT.java b/server/src/test/java/org/elasticsearch/index/shard/IndexShardIT.java
index 98664a56655..690ec48bcc6 100644
--- a/server/src/test/java/org/elasticsearch/index/shard/IndexShardIT.java
+++ b/server/src/test/java/org/elasticsearch/index/shard/IndexShardIT.java
@@ -85,7 +85,6 @@ import org.elasticsearch.test.ESSingleNodeTestCase;
 import org.elasticsearch.test.IndexSettingsModule;
 import org.elasticsearch.test.InternalSettingsPlugin;
 import org.elasticsearch.threadpool.ThreadPool;
-import org.elasticsearch.threadpool.ThreadPoolStats;
 import org.junit.Assert;
 
 import java.io.IOException;
@@ -102,6 +101,8 @@ import java.util.Locale;
 import java.util.concurrent.BrokenBarrierException;
 import java.util.concurrent.CountDownLatch;
 import java.util.concurrent.CyclicBarrier;
+import java.util.concurrent.Phaser;
+import java.util.concurrent.ThreadPoolExecutor;
 import java.util.concurrent.TimeUnit;
 import java.util.concurrent.TimeoutException;
 import java.util.concurrent.atomic.AtomicBoolean;
@@ -772,20 +773,28 @@ public class IndexShardIT extends ESSingleNodeTestCase {
         // wait for both to ensure we don't have in-flight operations
         updateSettingsLatch.await();
         refreshLatch.await();
-        // ensure no scheduled refresh to compete with the scheduleRefresh we are going to verify.
-        assertBusy(() -> {
-            for (ThreadPoolStats.Stats stat : indexService.getThreadPool().stats()) {
-                if (stat.getName().equals(ThreadPool.Names.REFRESH) && (stat.getQueue() > 0 || stat.getActive() > 0)) {
-                    throw new AssertionError(); // cause assert busy to retry
-                }
-            }
-        });
+        // We need to ensure a `scheduledRefresh` triggered by the internal refresh setting update is executed before we index a new doc;
+        // otherwise, it will compete to call `Engine#maybeRefresh` with the `scheduledRefresh` that we are going to verify.
+        ensureNoPendingScheduledRefresh(indexService.getThreadPool());
         client().prepareIndex("test", "test", "2").setSource("{\"foo\" : \"bar\"}", XContentType.JSON).get();
         assertTrue(shard.scheduledRefresh());
         assertTrue(shard.isSearchIdle());
         assertHitCount(client().prepareSearch().get(), 3);
     }
 
+    private void ensureNoPendingScheduledRefresh(ThreadPool threadPool) {
+        // We can make sure that all scheduled refresh tasks are done by submitting *maximumPoolSize* blocking tasks,
+        // then wait until all of them completed. Note that using ThreadPoolStats is not watertight as both queue and
+        // active count can be 0 when ThreadPoolExecutor just takes a task out the queue but before marking it active.
+        ThreadPoolExecutor refreshThreadPoolExecutor = (ThreadPoolExecutor) threadPool.executor(ThreadPool.Names.REFRESH);
+        int maximumPoolSize = refreshThreadPoolExecutor.getMaximumPoolSize();
+        Phaser barrier = new Phaser(maximumPoolSize + 1);
+        for (int i = 0; i < maximumPoolSize; i++) {
+            refreshThreadPoolExecutor.execute(barrier::arriveAndAwaitAdvance);
+        }
+        barrier.arriveAndAwaitAdvance();
+    }
+
     public void testGlobalCheckpointListeners() throws Exception {
         createIndex("test", Settings.builder()
             .put("index.number_of_shards", 1)