diff --git a/changelog/fragments/config-samples-kustomize-scaffold.yaml b/changelog/fragments/config-samples-kustomize-scaffold.yaml
new file mode 100644
index 00000000000..2378bdcd84f
--- /dev/null
+++ b/changelog/fragments/config-samples-kustomize-scaffold.yaml
@@ -0,0 +1,17 @@
+entries:
+  - description: >
+      Added a scaffold marker `+kubebuilder:scaffold:manifestskustomizesamples` to `config/samples/kustomization.yaml`
+      that allows updates without overwriting the entire file.
+    kind: change
+    breaking: true
+    migration:
+      header: Add the samples scaffold marker to your `config/samples/kustomization.yaml`
+      body: >
+        Add the `+kubebuilder:scaffold:manifestskustomizesamples` to your `config/samples/kustomization.yaml`
+        file like so (using an example sample file):
+
+        ```yaml
+        resources:
+        - cache_v1alpha1_memcached.yaml
+        # +kubebuilder:scaffold:manifestskustomizesamples
+        ```
diff --git a/internal/plugins/ansible/v1/api.go b/internal/plugins/ansible/v1/api.go
index 69f71cc0e5c..07397774555 100644
--- a/internal/plugins/ansible/v1/api.go
+++ b/internal/plugins/ansible/v1/api.go
@@ -117,7 +117,8 @@ func (p *createAPIPlugin) Run() error {
 
 // SDK phase 2 plugins.
 func (p *createAPIPlugin) runPhase2() error {
-	return manifests.RunCreateAPI(p.config)
+	gvk := p.createOptions.GVK
+	return manifests.RunCreateAPI(p.config, config.GVK{Group: gvk.Group, Version: gvk.Version, Kind: gvk.Kind})
 }
 
 func (p *createAPIPlugin) Validate() error {
diff --git a/internal/plugins/golang/v2/api.go b/internal/plugins/golang/v2/api.go
index e1b4a6ee9cd..6a2c5337244 100644
--- a/internal/plugins/golang/v2/api.go
+++ b/internal/plugins/golang/v2/api.go
@@ -39,6 +39,11 @@ func (p *createAPIPlugin) InjectConfig(c *config.Config) {
 }
 
 func (p *createAPIPlugin) Run() error {
+	// Run() may add a new resource to the config, so we can compare resources before/after to get the new resource.
+	oldResources := make(map[config.GVK]struct{}, len(p.config.Resources))
+	for _, r := range p.config.Resources {
+		oldResources[r] = struct{}{}
+	}
 	if err := p.CreateAPI.Run(); err != nil {
 		return err
 	}
@@ -49,11 +54,21 @@ func (p *createAPIPlugin) Run() error {
 		return nil
 	}
 
+	// Find the new resource. Here we shouldn't worry about checking if one was found, since downstream
+	// plugins will do so.
+	var newResource config.GVK
+	for _, r := range p.config.Resources {
+		if _, hasResource := oldResources[r]; !hasResource {
+			newResource = r
+			break
+		}
+	}
+
 	// Run SDK phase 2 plugins.
-	return p.runPhase2()
+	return p.runPhase2(newResource)
 }
 
 // SDK phase 2 plugins.
-func (p *createAPIPlugin) runPhase2() error {
-	return manifests.RunCreateAPI(p.config)
+func (p *createAPIPlugin) runPhase2(gvk config.GVK) error {
+	return manifests.RunCreateAPI(p.config, gvk)
 }
diff --git a/internal/plugins/helm/v1/api.go b/internal/plugins/helm/v1/api.go
index 29d3dc1cfc7..83873cd656b 100644
--- a/internal/plugins/helm/v1/api.go
+++ b/internal/plugins/helm/v1/api.go
@@ -137,7 +137,8 @@ func (p *createAPIPlugin) Run() error {
 
 // SDK phase 2 plugins.
 func (p *createAPIPlugin) runPhase2() error {
-	return manifests.RunCreateAPI(p.config)
+	gvk := p.createOptions.GVK
+	return manifests.RunCreateAPI(p.config, config.GVK{Group: gvk.Group, Version: gvk.Version, Kind: gvk.Kind})
 }
 
 // Validate perform the required validations for this plugin
diff --git a/internal/plugins/manifests/api.go b/internal/plugins/manifests/api.go
index d2c5a3c2d83..c6f9eabee1d 100644
--- a/internal/plugins/manifests/api.go
+++ b/internal/plugins/manifests/api.go
@@ -17,41 +17,53 @@ package manifests
 
 import (
 	"fmt"
-	"path/filepath"
-	"strings"
 
+	"sigs.k8s.io/kubebuilder/pkg/model"
 	"sigs.k8s.io/kubebuilder/pkg/model/config"
+	"sigs.k8s.io/kubebuilder/pkg/model/file"
 
-	"github.com/operator-framework/operator-sdk/internal/plugins/util/kustomize"
+	"github.com/operator-framework/operator-sdk/internal/kubebuilder/machinery"
 )
 
-// sampleKustomizationFragment is a template for samples/kustomization.yaml.
-const sampleKustomizationFragment = `## This file is auto-generated, do not modify ##
-resources:
-`
+// RunCreateAPI runs the manifests SDK phase 2 plugin.
+func RunCreateAPI(cfg *config.Config, gvk config.GVK) error {
 
-// RunCreateAPI perform the SDK plugin-specific scaffolds.
-func RunCreateAPI(cfg *config.Config) error {
-
-	// Write CR paths to the samples' kustomization file. This file has a
-	// "do not modify" comment so it is safe to overwrite.
-	samplesKustomization := sampleKustomizationFragment
-	for _, gvk := range cfg.Resources {
-		samplesKustomization += fmt.Sprintf("- %s\n", makeCRFileName(gvk))
-	}
-	kpath := filepath.Join("config", "samples")
-	if err := kustomize.Write(kpath, samplesKustomization); err != nil {
+	if err := newAPIScaffolder(cfg, gvk).scaffold(); err != nil {
 		return err
 	}
 
 	return nil
 }
 
-// todo(camilamacedo86): Now that we have the Kubebuilder scaffolding machinery included in our repo, we could make
-// this an actual template that supports both file.Template and file.Inserter for init and create api, respectively.
-// More info: https://github.com/operator-framework/operator-sdk/issues/3370
-// makeCRFileName returns a Custom Resource example file name in the same format
-// as kubebuilder's CreateAPI plugin for a gvk.
-func makeCRFileName(gvk config.GVK) string {
-	return fmt.Sprintf("%s_%s_%s.yaml", gvk.Group, gvk.Version, strings.ToLower(gvk.Kind))
+type apiScaffolder struct {
+	config *config.Config
+	gvk    config.GVK
+}
+
+func newAPIScaffolder(config *config.Config, gvk config.GVK) *apiScaffolder {
+	return &apiScaffolder{
+		config: config,
+		gvk:    gvk,
+	}
+}
+
+func (s *apiScaffolder) newUniverse() *model.Universe {
+	return model.NewUniverse(
+		model.WithConfig(s.config),
+	)
+}
+
+func (s *apiScaffolder) scaffold() error {
+	var builders []file.Builder
+	// If the gvk is non-empty, add relevant builders.
+	if s.gvk.Group != "" || s.gvk.Version != "" || s.gvk.Kind != "" {
+		builders = append(builders, &kustomization{GroupVersionKind: s.gvk})
+	}
+
+	err := machinery.NewScaffold().Execute(s.newUniverse(), builders...)
+	if err != nil {
+		return fmt.Errorf("error scaffolding manifests: %v", err)
+	}
+
+	return nil
 }
diff --git a/internal/plugins/manifests/samples.go b/internal/plugins/manifests/samples.go
new file mode 100644
index 00000000000..65e9ca5f5d0
--- /dev/null
+++ b/internal/plugins/manifests/samples.go
@@ -0,0 +1,75 @@
+// Copyright 2020 The Operator-SDK Authors
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+package manifests
+
+import (
+	"fmt"
+	"path/filepath"
+	"strings"
+
+	"sigs.k8s.io/kubebuilder/pkg/model/config"
+	"sigs.k8s.io/kubebuilder/pkg/model/file"
+)
+
+var _ file.Template = &kustomization{}
+var _ file.Inserter = &kustomization{}
+
+// kustomization scaffolds or updates the kustomization.yaml in config/samples.
+type kustomization struct {
+	file.TemplateMixin
+
+	// GroupVersionKind is the sample's gvk to add to this scaffold.
+	GroupVersionKind config.GVK
+}
+
+// SetTemplateDefaults implements file.Template
+func (f *kustomization) SetTemplateDefaults() error {
+	if f.Path == "" {
+		f.Path = filepath.Join("config", "samples", "kustomization.yaml")
+	}
+
+	f.TemplateBody = fmt.Sprintf(kustomizationTemplate, file.NewMarkerFor(f.Path, samplesMarker))
+
+	return nil
+}
+
+const (
+	samplesMarker = "manifestskustomizesamples"
+)
+
+// GetMarkers implements file.Inserter
+func (f *kustomization) GetMarkers() []file.Marker {
+	return []file.Marker{file.NewMarkerFor(f.Path, samplesMarker)}
+}
+
+const samplesCodeFragment = `- %s
+`
+
+// makeCRFileName returns a Custom Resource example file name in the same format
+// as kubebuilder's CreateAPI plugin for a gvk.
+func makeCRFileName(gvk config.GVK) string {
+	return fmt.Sprintf("%s_%s_%s.yaml", gvk.Group, gvk.Version, strings.ToLower(gvk.Kind))
+}
+
+// GetCodeFragments implements file.Inserter
+func (f *kustomization) GetCodeFragments() file.CodeFragmentsMap {
+	return file.CodeFragmentsMap{
+		file.NewMarkerFor(f.Path, samplesMarker): []string{fmt.Sprintf(samplesCodeFragment, makeCRFileName(f.GroupVersionKind))},
+	}
+}
+
+const kustomizationTemplate = `## Append samples you want in your CSV to this file as resources ##
+resources:
+%s
+`