diff --git a/pkg/transformers/labelsandannotations_test.go b/pkg/transformers/labelsandannotations_test.go
index f0609d3f9..d4886f9b0 100644
--- a/pkg/transformers/labelsandannotations_test.go
+++ b/pkg/transformers/labelsandannotations_test.go
@@ -31,6 +31,7 @@ var cmap = schema.GroupVersionKind{Version: "v1", Kind: "ConfigMap"}
 var deploy = schema.GroupVersionKind{Group: "apps", Version: "v1", Kind: "Deployment"}
 var statefulset = schema.GroupVersionKind{Group: "apps", Version: "v1", Kind: "StatefulSet"}
 var foo = schema.GroupVersionKind{Group: "example.com", Version: "v1", Kind: "Foo"}
+var crd = schema.GroupVersionKind{Group: "apiwctensions.k8s.io", Version: "v1beta1", Kind: "CustomResourceDefinition"}
 
 func TestLabelsRun(t *testing.T) {
 	m := resmap.ResMap{
diff --git a/pkg/transformers/prefixname.go b/pkg/transformers/prefixname.go
index 81e1608c9..7632f6396 100644
--- a/pkg/transformers/prefixname.go
+++ b/pkg/transformers/prefixname.go
@@ -21,13 +21,16 @@ import (
 	"fmt"
 
 	"github.com/kubernetes-sigs/kustomize/pkg/resmap"
+
+	"k8s.io/apimachinery/pkg/runtime/schema"
 )
 
 // namePrefixTransformer contains the prefix and the path config for each field that
 // the name prefix will be applied.
 type namePrefixTransformer struct {
-	prefix      string
-	pathConfigs []PathConfig
+	prefix          string
+	pathConfigs     []PathConfig
+	skipPathConfigs []PathConfig
 }
 
 var _ Transformer = &namePrefixTransformer{}
@@ -39,6 +42,12 @@ var defaultNamePrefixPathConfigs = []PathConfig{
 	},
 }
 
+var skipNamePrefixPathConfigs = []PathConfig{
+	{
+		GroupVersionKind: &schema.GroupVersionKind{Kind: "CustomResourceDefinition"},
+	},
+}
+
 // NewDefaultingNamePrefixTransformer construct a namePrefixTransformer with defaultNamePrefixPathConfigs.
 func NewDefaultingNamePrefixTransformer(nameprefix string) (Transformer, error) {
 	return NewNamePrefixTransformer(defaultNamePrefixPathConfigs, nameprefix)
@@ -52,13 +61,25 @@ func NewNamePrefixTransformer(pc []PathConfig, np string) (Transformer, error) {
 	if pc == nil {
 		return nil, errors.New("pathConfigs is not expected to be nil")
 	}
-	return &namePrefixTransformer{pathConfigs: pc, prefix: np}, nil
+	return &namePrefixTransformer{pathConfigs: pc, prefix: np, skipPathConfigs: skipNamePrefixPathConfigs}, nil
 }
 
 // Transform prepends the name prefix.
 func (o *namePrefixTransformer) Transform(m resmap.ResMap) error {
+	mf := resmap.ResMap{}
+
 	for id := range m {
-		objMap := m[id].UnstructuredContent()
+		mf[id] = m[id]
+		for _, path := range o.skipPathConfigs {
+			if selectByGVK(id.Gvk(), path.GroupVersionKind) {
+				delete(mf, id)
+				break
+			}
+		}
+	}
+
+	for id := range mf {
+		objMap := mf[id].UnstructuredContent()
 		for _, path := range o.pathConfigs {
 			if !selectByGVK(id.Gvk(), path.GroupVersionKind) {
 				continue
diff --git a/pkg/transformers/prefixname_test.go b/pkg/transformers/prefixname_test.go
index a9f3fa175..b0aa9d1ea 100644
--- a/pkg/transformers/prefixname_test.go
+++ b/pkg/transformers/prefixname_test.go
@@ -42,6 +42,14 @@ func TestPrefixNameRun(t *testing.T) {
 					"name": "cm2",
 				},
 			}),
+		resource.NewResId(crd, "crd"): resource.NewResourceFromMap(
+			map[string]interface{}{
+				"apiVersion": "apiextensions.k8s.io/v1beta1",
+				"kind":       "CustomResourceDefinition",
+				"metadata": map[string]interface{}{
+					"name": "crd",
+				},
+			}),
 	}
 	expected := resmap.ResMap{
 		resource.NewResId(cmap, "cm1"): resource.NewResourceFromMap(
@@ -60,6 +68,14 @@ func TestPrefixNameRun(t *testing.T) {
 					"name": "someprefix-cm2",
 				},
 			}),
+		resource.NewResId(crd, "crd"): resource.NewResourceFromMap(
+			map[string]interface{}{
+				"apiVersion": "apiextensions.k8s.io/v1beta1",
+				"kind":       "CustomResourceDefinition",
+				"metadata": map[string]interface{}{
+					"name": "crd",
+				},
+			}),
 	}
 
 	npt, err := NewDefaultingNamePrefixTransformer("someprefix-")