diff --git a/cmd/flux/build_kustomization.go b/cmd/flux/build_kustomization.go
index 507fb94c..ee29edc7 100644
--- a/cmd/flux/build_kustomization.go
+++ b/cmd/flux/build_kustomization.go
@@ -21,10 +21,12 @@ import (
 	"os"
 	"os/signal"
 
+	"github.com/fluxcd/pkg/ssa"
 	"github.com/spf13/cobra"
 
-	"github.com/fluxcd/flux2/v2/internal/build"
 	kustomizev1 "github.com/fluxcd/kustomize-controller/api/v1"
+
+	"github.com/fluxcd/flux2/v2/internal/build"
 )
 
 var buildKsCmd = &cobra.Command{
@@ -114,12 +116,17 @@ func buildKsCmdRun(cmd *cobra.Command, args []string) (err error) {
 
 	errChan := make(chan error)
 	go func() {
-		manifests, err := builder.Build()
+		objects, err := builder.Build()
+		if err != nil {
+			errChan <- err
+		}
+
+		manifests, err := ssa.ObjectsToYAML(objects)
 		if err != nil {
 			errChan <- err
 		}
 
-		cmd.Print(string(manifests))
+		cmd.Print(manifests)
 		errChan <- nil
 	}()
 
diff --git a/cmd/flux/testdata/build-kustomization/podinfo-result.yaml b/cmd/flux/testdata/build-kustomization/podinfo-result.yaml
index 009347d8..bf162251 100644
--- a/cmd/flux/testdata/build-kustomization/podinfo-result.yaml
+++ b/cmd/flux/testdata/build-kustomization/podinfo-result.yaml
@@ -171,3 +171,4 @@ metadata:
   name: db-user-pass-bkbd782d2c
   namespace: default
 type: Opaque
+---
diff --git a/cmd/flux/testdata/build-kustomization/podinfo-with-var-substitution-result.yaml b/cmd/flux/testdata/build-kustomization/podinfo-with-var-substitution-result.yaml
index 0c32c936..01686566 100644
--- a/cmd/flux/testdata/build-kustomization/podinfo-with-var-substitution-result.yaml
+++ b/cmd/flux/testdata/build-kustomization/podinfo-with-var-substitution-result.yaml
@@ -214,3 +214,4 @@ metadata:
     kustomize.toolkit.fluxcd.io/substitute: disabled
   name: flux-grafana-dashboards-kt8md725kf
   namespace: default
+---
diff --git a/cmd/flux/testdata/build-kustomization/podinfo-without-service-result.yaml b/cmd/flux/testdata/build-kustomization/podinfo-without-service-result.yaml
index e1e1885f..647ce020 100644
--- a/cmd/flux/testdata/build-kustomization/podinfo-without-service-result.yaml
+++ b/cmd/flux/testdata/build-kustomization/podinfo-without-service-result.yaml
@@ -99,3 +99,4 @@ spec:
     apiVersion: apps/v1
     kind: Deployment
     name: podinfo
+---
diff --git a/internal/build/build.go b/internal/build/build.go
index 083a7ca4..0f2f1ca4 100644
--- a/internal/build/build.go
+++ b/internal/build/build.go
@@ -28,6 +28,7 @@ import (
 	"sync"
 	"time"
 
+	"github.com/fluxcd/pkg/ssa"
 	"github.com/theckman/yacspin"
 	"k8s.io/apimachinery/pkg/api/meta"
 	"k8s.io/apimachinery/pkg/apis/meta/v1/unstructured"
@@ -212,7 +213,7 @@ func (b *Builder) getKustomization(ctx context.Context) (*kustomizev1.Kustomizat
 // and overlays the manifests with the resources specified in the resourcesPath
 // It expects a kustomization.yaml file in the resourcesPath, and it will
 // generate a kustomization.yaml file if it doesn't exist
-func (b *Builder) Build() ([]byte, error) {
+func (b *Builder) Build() ([]*unstructured.Unstructured, error) {
 	m, err := b.build()
 	if err != nil {
 		return nil, err
@@ -223,7 +224,16 @@ func (b *Builder) Build() ([]byte, error) {
 		return nil, fmt.Errorf("kustomize build failed: %w", err)
 	}
 
-	return resources, nil
+	objects, err := ssa.ReadObjects(bytes.NewReader(resources))
+	if err != nil {
+		return nil, fmt.Errorf("kustomize build failed: %w", err)
+	}
+
+	if m := b.kustomization.Spec.CommonMetadata; m != nil {
+		ssa.SetCommonMetadata(objects, m.Labels, m.Annotations)
+	}
+
+	return objects, nil
 }
 
 func (b *Builder) build() (m resmap.ResMap, err error) {
diff --git a/internal/build/diff.go b/internal/build/diff.go
index b510b129..e693e1d9 100644
--- a/internal/build/diff.go
+++ b/internal/build/diff.go
@@ -39,10 +39,10 @@ import (
 	"sigs.k8s.io/cli-utils/pkg/object"
 	"sigs.k8s.io/yaml"
 
+	kustomizev1 "github.com/fluxcd/kustomize-controller/api/v1"
 	"github.com/fluxcd/pkg/ssa"
 
 	"github.com/fluxcd/flux2/v2/pkg/printers"
-	kustomizev1 "github.com/fluxcd/kustomize-controller/api/v1"
 )
 
 func (b *Builder) Manager() (*ssa.ResourceManager, error) {
@@ -58,12 +58,12 @@ func (b *Builder) Manager() (*ssa.ResourceManager, error) {
 func (b *Builder) Diff() (string, bool, error) {
 	output := strings.Builder{}
 	createdOrDrifted := false
-	res, err := b.Build()
+	objects, err := b.Build()
 	if err != nil {
 		return "", createdOrDrifted, err
 	}
-	// convert the build result into Kubernetes unstructured objects
-	objects, err := ssa.ReadObjects(bytes.NewReader(res))
+
+	err = ssa.SetNativeKindsDefaults(objects)
 	if err != nil {
 		return "", createdOrDrifted, err
 	}
@@ -76,10 +76,6 @@ func (b *Builder) Diff() (string, bool, error) {
 	ctx, cancel := context.WithTimeout(context.Background(), b.timeout)
 	defer cancel()
 
-	if err := ssa.SetNativeKindsDefaults(objects); err != nil {
-		return "", createdOrDrifted, err
-	}
-
 	if b.spinner != nil {
 		err = b.spinner.Start()
 		if err != nil {