diff --git a/qa/full-cluster-restart/src/test/java/org/elasticsearch/upgrades/FullClusterRestartIT.java b/qa/full-cluster-restart/src/test/java/org/elasticsearch/upgrades/FullClusterRestartIT.java
index 57c6ad7ff86..081a1918674 100644
--- a/qa/full-cluster-restart/src/test/java/org/elasticsearch/upgrades/FullClusterRestartIT.java
+++ b/qa/full-cluster-restart/src/test/java/org/elasticsearch/upgrades/FullClusterRestartIT.java
@@ -24,7 +24,9 @@ import org.apache.http.entity.ContentType;
 import org.apache.http.entity.StringEntity;
 import org.apache.http.util.EntityUtils;
 import org.elasticsearch.Version;
+import org.elasticsearch.client.Request;
 import org.elasticsearch.client.Response;
+import org.elasticsearch.client.ResponseException;
 import org.elasticsearch.client.RestClient;
 import org.elasticsearch.cluster.metadata.IndexMetaData;
 import org.elasticsearch.common.Booleans;
@@ -701,8 +703,24 @@ public class FullClusterRestartIT extends ESRestTestCase {
 
             // make sure all recoveries are done
             ensureGreen(index);
-            // Explicitly flush so we're sure to have a bunch of documents in the Lucene index
-            client().performRequest("POST", "/_flush");
+            // Recovering a synced-flush index from 5.x to 6.x might be subtle as a 5.x index commit does not have all 6.x commit tags.
+            if (randomBoolean()) {
+                // We have to spin synced-flush requests here because we fire the global checkpoint sync for the last write operation.
+                // A synced-flush request considers the global checkpoint sync as an going operation because it acquires a shard permit.
+                assertBusy(() -> {
+                    try {
+                        Response resp = client().performRequest(new Request("POST", index + "/_flush/synced"));
+                        Map<String, Object> result = ObjectPath.createFromResponse(resp).evaluate("_shards");
+                        assertThat(result.get("successful"), equalTo(result.get("total")));
+                        assertThat(result.get("failed"), equalTo(0));
+                    } catch (ResponseException ex) {
+                        throw new AssertionError(ex); // cause assert busy to retry
+                    }
+                });
+            } else {
+                // Explicitly flush so we're sure to have a bunch of documents in the Lucene index
+                assertOK(client().performRequest(new Request("POST", "/_flush")));
+            }
             if (shouldHaveTranslog) {
                 // Update a few documents so we are sure to have a translog
                 indexRandomDocuments(count / 10, false /* Flushing here would invalidate the whole thing....*/, false,
diff --git a/qa/rolling-upgrade/src/test/java/org/elasticsearch/upgrades/RecoveryIT.java b/qa/rolling-upgrade/src/test/java/org/elasticsearch/upgrades/RecoveryIT.java
index 1351de16cf7..809cd40d698 100644
--- a/qa/rolling-upgrade/src/test/java/org/elasticsearch/upgrades/RecoveryIT.java
+++ b/qa/rolling-upgrade/src/test/java/org/elasticsearch/upgrades/RecoveryIT.java
@@ -22,7 +22,9 @@ import org.apache.http.entity.ContentType;
 import org.apache.http.entity.StringEntity;
 import org.elasticsearch.Version;
 import org.elasticsearch.action.support.PlainActionFuture;
+import org.elasticsearch.client.Request;
 import org.elasticsearch.client.Response;
+import org.elasticsearch.client.ResponseException;
 import org.elasticsearch.cluster.metadata.IndexMetaData;
 import org.elasticsearch.common.settings.Settings;
 import org.elasticsearch.common.util.concurrent.AbstractRunnable;
@@ -239,4 +241,34 @@ public class RecoveryIT extends AbstractRollingTestCase {
         }
     }
 
+    public void testRecoverSyncedFlushIndex() throws Exception {
+        final String index = "recover_synced_flush_index";
+        if (CLUSTER_TYPE == ClusterType.OLD) {
+            Settings.Builder settings = Settings.builder()
+                .put(IndexMetaData.INDEX_NUMBER_OF_SHARDS_SETTING.getKey(), 1)
+                .put(IndexMetaData.INDEX_NUMBER_OF_REPLICAS_SETTING.getKey(), 1)
+                // if the node with the replica is the first to be restarted, while a replica is still recovering
+                // then delayed allocation will kick in. When the node comes back, the master will search for a copy
+                // but the recovering copy will be seen as invalid and the cluster health won't return to GREEN
+                // before timing out
+                .put(INDEX_DELAYED_NODE_LEFT_TIMEOUT_SETTING.getKey(), "100ms")
+                .put(SETTING_ALLOCATION_MAX_RETRY.getKey(), "0"); // fail faster
+            createIndex(index, settings.build());
+            indexDocs(index, 0, randomInt(5));
+            // We have to spin synced-flush requests here because we fire the global checkpoint sync for the last write operation.
+            // A synced-flush request considers the global checkpoint sync as an going operation because it acquires a shard permit.
+            assertBusy(() -> {
+                try {
+                    Response resp = client().performRequest(new Request("POST", index + "/_flush/synced"));
+                    Map<String, Object> result = ObjectPath.createFromResponse(resp).evaluate("_shards");
+                    assertThat(result.get("successful"), equalTo(result.get("total")));
+                    assertThat(result.get("failed"), equalTo(0));
+                } catch (ResponseException ex) {
+                    throw new AssertionError(ex); // cause assert busy to retry
+                }
+            });
+        }
+        ensureGreen(index);
+    }
+
 }