diff --git a/integration/render_test.go b/integration/render_test.go
index ef16dadf551..a1794f7be94 100644
--- a/integration/render_test.go
+++ b/integration/render_test.go
@@ -60,6 +60,8 @@ spec:
 `,
 		expectedOut: fmt.Sprintf(`apiVersion: v1
 kind: Pod
+metadata:
+  namespace: %s
 spec:
   containers:
   - image: gcr.io/k8s-skaffold/skaffold:test
@@ -179,8 +181,6 @@ spec:
 ---
 apiVersion: v1
 kind: Pod
-metadata:
-  name: my-pod-456
 spec:
   containers:
   - image: gcr.io/project/image2
@@ -199,7 +199,6 @@ spec:
 apiVersion: v1
 kind: Pod
 metadata:
-  name: my-pod-456
   namespace: %s
 spec:
   containers:
diff --git a/pkg/skaffold/kubernetes/manifest/namespace_test.go b/pkg/skaffold/kubernetes/manifest/namespace_test.go
index 7a7bbfbc569..a40054460d2 100644
--- a/pkg/skaffold/kubernetes/manifest/namespace_test.go
+++ b/pkg/skaffold/kubernetes/manifest/namespace_test.go
@@ -306,7 +306,7 @@ spec:
 			description: "unexpected metadata type",
 			namespace:   "test",
 			manifests:   ManifestList{[]byte(`metadata: []`)},
-			expected:    ManifestList{[]byte(`metadata: []`)},
+			shouldErr:   true,
 		},
 		{
 			description: "single Pod manifest in the list with same namespace as set",
diff --git a/pkg/skaffold/kubernetes/manifest/namespaces.go b/pkg/skaffold/kubernetes/manifest/namespaces.go
index 70d8356ca7a..860032e645d 100644
--- a/pkg/skaffold/kubernetes/manifest/namespaces.go
+++ b/pkg/skaffold/kubernetes/manifest/namespaces.go
@@ -25,8 +25,11 @@ import (
 	"k8s.io/apimachinery/pkg/runtime/schema"
 
 	"github.com/GoogleContainerTools/skaffold/pkg/skaffold/output/log"
+	"github.com/GoogleContainerTools/skaffold/pkg/skaffold/yaml"
 )
 
+const namespaceField = "namespace"
+
 // CollectNamespaces returns all the namespaces in the manifests.
 func (l *ManifestList) CollectNamespaces() ([]string, error) {
 	replacer := newNamespaceCollector()
@@ -66,7 +69,7 @@ func (r *namespaceCollector) Visit(gk schema.GroupKind, navpath string, o map[st
 	if !ok {
 		return true
 	}
-	if nsValue, present := metadata["namespace"]; present {
+	if nsValue, present := metadata[namespaceField]; present {
 		nsString, ok := nsValue.(string)
 		if !ok || nsString == "" {
 			return true
@@ -84,49 +87,48 @@ func (l *ManifestList) SetNamespace(namespace string, rs ResourceSelector) (Mani
 	if namespace == "" {
 		return *l, nil
 	}
-	replacer := newNamespaceSetter(namespace)
-	updated, err := l.Visit(replacer, rs)
-	if err != nil {
-		return nil, nsSettingErr(err)
-	}
-	if replacer.inValid {
-		return nil, nsAlreadySetErr()
+	var updated ManifestList
+	for _, item := range *l {
+		m := make(map[string]interface{})
+		if err := yaml.Unmarshal(item, &m); err != nil {
+			return nil, fmt.Errorf("reading Kubernetes YAML: %w", err)
+		}
+		if len(m) == 0 {
+			continue
+		}
+		if errU := addOrUpdateNamespace(m, namespace); errU != nil {
+			return nil, errU
+		}
+		updatedManifest, err := yaml.Marshal(m)
+		if err != nil {
+			return nil, nsSettingErr(err)
+		}
+
+		updated = append(updated, updatedManifest)
 	}
 
 	log.Entry(context.TODO()).Debugln("manifests set with namespace", updated.String())
-
 	return updated, nil
 }
 
-type namespaceSetter struct {
-	ns      string
-	inValid bool
-}
-
-func newNamespaceSetter(ns string) *namespaceSetter {
-	return &namespaceSetter{
-		ns:      ns,
-		inValid: false,
-	}
-}
-
-func (r *namespaceSetter) Visit(gk schema.GroupKind, navpath string, o map[string]interface{}, k string, v interface{}, rs ResourceSelector) bool {
-	if k != metadataField {
-		return true
+func addOrUpdateNamespace(manifest map[string]interface{}, ns string) error {
+	originalMetadata, ok := manifest[metadataField]
+	if !ok {
+		metadataAdded := make(map[string]interface{})
+		metadataAdded[namespaceField] = ns
+		manifest[metadataField] = metadataAdded
+		return nil
 	}
-
-	metadata, ok := v.(map[string]interface{})
+	metadata, ok := originalMetadata.(map[string]interface{})
 	if !ok {
-		return true
+		return nsSettingErr(fmt.Errorf("error converting %s to map[string]interface{}", originalMetadata))
 	}
-
-	nsValue, present := metadata["namespace"]
-	if !present || isEmptyOrEqual(nsValue, r.ns) {
-		metadata["namespace"] = r.ns
-		return false
+	nsValue, present := metadata[namespaceField]
+	if !present || isEmptyOrEqual(nsValue, ns) {
+		metadata[namespaceField] = ns
+		return nil
 	}
-	r.inValid = true
-	return false
+	return nsAlreadySetErr()
 }
 
 func isEmptyOrEqual(v interface{}, s string) bool {