diff --git a/server/src/main/java/org/elasticsearch/gateway/GatewayMetaState.java b/server/src/main/java/org/elasticsearch/gateway/GatewayMetaState.java
index bd6fd908d49..30361fa70ee 100644
--- a/server/src/main/java/org/elasticsearch/gateway/GatewayMetaState.java
+++ b/server/src/main/java/org/elasticsearch/gateway/GatewayMetaState.java
@@ -320,7 +320,14 @@ public class GatewayMetaState implements ClusterStateApplier, CoordinationState.
                 finished = true;
                 return generation;
             } catch (WriteStateException e) {
-                rollback();
+                // if Manifest write results in dirty WriteStateException it's not safe to remove
+                // new metadata files, because if Manifest was actually written to disk and its deletion
+                // fails it will reference these new metadata files.
+                // In the future, we might decide to add more fine grained check to understand if after
+                // WriteStateException Manifest deletion has actually failed.
+                if (e.isDirty() == false) {
+                    rollback();
+                }
                 throw e;
             }
         }
diff --git a/server/src/test/java/org/elasticsearch/gateway/GatewayMetaStateTests.java b/server/src/test/java/org/elasticsearch/gateway/GatewayMetaStateTests.java
index 1f4e0bafe4a..22259b919ec 100644
--- a/server/src/test/java/org/elasticsearch/gateway/GatewayMetaStateTests.java
+++ b/server/src/test/java/org/elasticsearch/gateway/GatewayMetaStateTests.java
@@ -374,7 +374,6 @@ public class GatewayMetaStateTests extends ESAllocationTestCase {
         return builder.build();
     }
 
-    @AwaitsFix(bugUrl = "https://github.com/elastic/elasticsearch/issues/39077")
     public void testAtomicityWithFailures() throws IOException {
         try (NodeEnvironment env = newNodeEnvironment()) {
             MetaStateServiceWithFailures metaStateService =