diff --git a/api/krusty/namereference_test.go b/api/krusty/namereference_test.go
index 806cad1b3..293746571 100644
--- a/api/krusty/namereference_test.go
+++ b/api/krusty/namereference_test.go
@@ -649,7 +649,6 @@ metadata:
   name: oldNs
 `)
 	m := th.Run(".", th.MakeDefaultOptions())
-	// Incorrect: the self-reference annotations in both resources were not updated!
 	th.AssertActualEqualsExpected(m, `
 apiVersion: v1
 data:
@@ -658,7 +657,7 @@ data:
 kind: ConfigMap
 metadata:
   annotations:
-    theConfigMap: cm
+    theConfigMap: cm-updated
     theNamespace: newNs
   name: cm-updated
   namespace: newNs
@@ -668,7 +667,7 @@ kind: Namespace
 metadata:
   annotations:
     theConfigMap: cm-updated
-    theNamespace: oldNs
+    theNamespace: newNs
   name: newNs
 `)
 }
diff --git a/api/resource/resource.go b/api/resource/resource.go
index 9997e408b..a88ce31d2 100644
--- a/api/resource/resource.go
+++ b/api/resource/resource.go
@@ -255,13 +255,9 @@ func (r *Resource) appendCsvAnnotation(name, value string) {
 	if value == "" {
 		return
 	}
-	annotations := r.GetAnnotations()
-	if existing, ok := annotations[name]; ok {
-		annotations[name] = existing + "," + value
-	} else {
-		annotations[name] = value
-	}
-	if err := r.SetAnnotations(annotations); err != nil {
+	currentValue := r.getCsvAnnotation(name)
+	newValue := strings.Join(append(currentValue, value), ",")
+	if err := r.RNode.PipeE(kyaml.SetAnnotation(name, newValue)); err != nil {
 		panic(err)
 	}
 }
diff --git a/api/resource/resource_test.go b/api/resource/resource_test.go
index 106c827ae..8e2b692ed 100644
--- a/api/resource/resource_test.go
+++ b/api/resource/resource_test.go
@@ -1402,31 +1402,31 @@ spec:
 `))
 	assert.NoError(t, err)
 	r.AppendRefBy(resid.FromString("knd1.ver1.gr1/name1.ns1"))
-	assert.Equal(t, r.RNode.MustString(), `apiVersion: v1
+	assert.Equal(t, `apiVersion: v1
 kind: Deployment
 metadata:
   name: clown
   annotations:
-    internal.config.kubernetes.io/refBy: knd1.ver1.gr1/name1.ns1
+    internal.config.kubernetes.io/refBy: 'knd1.ver1.gr1/name1.ns1'
 spec:
   numReplicas: 1
-`)
+`, r.RNode.MustString())
 	assert.Equal(t, r.GetRefBy(), []resid.ResId{resid.FromString("knd1.ver1.gr1/name1.ns1")})
 
 	r.AppendRefBy(resid.FromString("knd2.ver2.gr2/name2.ns2"))
-	assert.Equal(t, r.RNode.MustString(), `apiVersion: v1
+	assert.Equal(t, `apiVersion: v1
 kind: Deployment
 metadata:
   name: clown
   annotations:
-    internal.config.kubernetes.io/refBy: knd1.ver1.gr1/name1.ns1,knd2.ver2.gr2/name2.ns2
+    internal.config.kubernetes.io/refBy: 'knd1.ver1.gr1/name1.ns1,knd2.ver2.gr2/name2.ns2'
 spec:
   numReplicas: 1
-`)
-	assert.Equal(t, r.GetRefBy(), []resid.ResId{
+`, r.RNode.MustString())
+	assert.Equal(t, []resid.ResId{
 		resid.FromString("knd1.ver1.gr1/name1.ns1"),
 		resid.FromString("knd2.ver2.gr2/name2.ns2"),
-	})
+	}, r.GetRefBy())
 }
 
 func TestOrigin(t *testing.T) {