diff --git a/controller/appcontroller.go b/controller/appcontroller.go
index edd7e347f45d8..2e1359a468212 100644
--- a/controller/appcontroller.go
+++ b/controller/appcontroller.go
@@ -284,12 +284,8 @@ func (ctrl *ApplicationController) handleObjectUpdated(managedByApp map[string]b
 				if !ok {
 					continue
 				}
-				// exclude resource unless it is permitted in the app project. If project is not permitted then it is not controlled by the user and there is no point showing the warning.
-				if proj, err := ctrl.getAppProj(app); err == nil && proj.IsGroupKindPermitted(ref.GroupVersionKind().GroupKind(), true) &&
-					!isKnownOrphanedResourceExclusion(kube.NewResourceKey(ref.GroupVersionKind().Group, ref.GroupVersionKind().Kind, ref.Namespace, ref.Name), proj) {
 
-					managedByApp[app.Name] = false
-				}
+				managedByApp[app.Name] = true
 			}
 		}
 	}
@@ -1638,7 +1634,7 @@ func (ctrl *ApplicationController) newApplicationInformerAndLister() (cache.Shar
 					return nil, nil
 				}
 
-				proj, err := ctrl.getAppProj(app)
+				proj, err := applisters.NewAppProjectLister(ctrl.projInformer.GetIndexer()).AppProjects(ctrl.namespace).Get(app.Spec.GetProject())
 				if err != nil {
 					return nil, nil
 				}
diff --git a/controller/appcontroller_test.go b/controller/appcontroller_test.go
index 3a55fc6419523..e7119c8bc13f7 100644
--- a/controller/appcontroller_test.go
+++ b/controller/appcontroller_test.go
@@ -785,11 +785,11 @@ func TestHandleOrphanedResourceUpdated(t *testing.T) {
 
 	isRequested, level := ctrl.isRefreshRequested(app1.Name)
 	assert.True(t, isRequested)
-	assert.Equal(t, ComparisonWithNothing, level)
+	assert.Equal(t, CompareWithRecent, level)
 
 	isRequested, level = ctrl.isRefreshRequested(app2.Name)
 	assert.True(t, isRequested)
-	assert.Equal(t, ComparisonWithNothing, level)
+	assert.Equal(t, CompareWithRecent, level)
 }
 
 func TestGetResourceTree_HasOrphanedResources(t *testing.T) {