diff --git a/plugin/src/main/java/org/elasticsearch/xpack/ml/job/persistence/JobStorageDeletionTask.java b/plugin/src/main/java/org/elasticsearch/xpack/ml/job/persistence/JobStorageDeletionTask.java
index f7d84e8d2c6..2af33c9899a 100644
--- a/plugin/src/main/java/org/elasticsearch/xpack/ml/job/persistence/JobStorageDeletionTask.java
+++ b/plugin/src/main/java/org/elasticsearch/xpack/ml/job/persistence/JobStorageDeletionTask.java
@@ -114,6 +114,7 @@ public class JobStorageDeletionTask extends Task {
         searchRequest.source(new SearchSourceBuilder().query(query));
         searchRequest.indicesOptions(JobProvider.addIgnoreUnavailable(IndicesOptions.lenientExpandOpen()));
         request.setAbortOnVersionConflict(false);
+        request.setRefresh(true);
 
         client.execute(DeleteByQueryAction.INSTANCE, request, ActionListener.wrap(
                 response -> finishedHandler.onResponse(true),
@@ -149,6 +150,7 @@ public class JobStorageDeletionTask extends Task {
         searchRequest.source(new SearchSourceBuilder().query(query));
         searchRequest.indicesOptions(JobProvider.addIgnoreUnavailable(IndicesOptions.lenientExpandOpen()));
         request.setAbortOnVersionConflict(false);
+        request.setRefresh(true);
 
         client.execute(DeleteByQueryAction.INSTANCE, request, ActionListener.wrap(
                 response -> {
diff --git a/plugin/src/test/resources/rest-api-spec/test/ml/index_layout.yml b/plugin/src/test/resources/rest-api-spec/test/ml/index_layout.yml
index 66cb59a755d..28d4ea804aa 100644
--- a/plugin/src/test/resources/rest-api-spec/test/ml/index_layout.yml
+++ b/plugin/src/test/resources/rest-api-spec/test/ml/index_layout.yml
@@ -180,9 +180,6 @@
         index: ".ml-anomalies-shared"
   - is_true: ''
 
-  - do:
-      indices.refresh: {}
-
   - do:
       count:
         index: .ml-state
@@ -249,9 +246,6 @@
         index: ".ml-anomalies-index-layout-job2"
   - is_false: ''
 
-  - do:
-      indices.refresh: {}
-
   - do:
       count:
         type: doc
@@ -379,9 +373,6 @@
         index: "foo"
   - is_true: ''
 
-  - do:
-      indices.refresh: {}
-
   - do:
       count:
         index: .ml-state
@@ -392,6 +383,9 @@
         index: .ml-anomalies-shared
   - match: {count: 0}
 
+  - do:
+      indices.refresh: {}
+
   - do:
       count:
         index: foo
@@ -436,9 +430,6 @@
         job_id: "index-layout-quantiles-job"
   - match: { acknowledged: true }
 
-  - do:
-      indices.refresh: {}
-
   - do:
       count:
         index: .ml-state
@@ -509,17 +500,11 @@
         body:
           state: more-new-categorizer-state
 
-  - do:
-      indices.refresh: {}
-
   - do:
       xpack.ml.delete_job:
         job_id: "index-layout-state-job"
   - match: { acknowledged: true }
 
-  - do:
-      indices.refresh: {}
-
   - do:
       count:
         index: .ml-anomalies-shared