diff --git a/integration/helm_test.go b/integration/helm_test.go
index d95bab12060..ec694ac3a28 100644
--- a/integration/helm_test.go
+++ b/integration/helm_test.go
@@ -33,10 +33,10 @@ func TestHelmDeploy(t *testing.T) {
 	env := []string{fmt.Sprintf("TEST_NS=%s", ns.Name)}
 	skaffold.Deploy("--images", "gcr.io/k8s-skaffold/skaffold-helm").InDir("testdata/helm").InNs(ns.Name).WithEnv(env).RunOrFail(t)
 
-	// check if labels are set correctly for deployment
+	// check if annotations are set correctly for deployment
 	dep := client.GetDeployment("skaffold-helm-" + ns.Name)
 	testutil.CheckDeepEqual(t, dep.Name, dep.ObjectMeta.Labels["release"])
-	testutil.CheckDeepEqual(t, "helm", dep.ObjectMeta.Labels["skaffold.dev/deployer"])
+	testutil.CheckDeepEqual(t, "helm", dep.ObjectMeta.Annotations["skaffold.dev/deployer"])
 
 	skaffold.Delete().InDir("testdata/helm").InNs(ns.Name).WithEnv(env).RunOrFail(t)
 }
diff --git a/integration/render_test.go b/integration/render_test.go
index 773081848af..3896cf27068 100644
--- a/integration/render_test.go
+++ b/integration/render_test.go
@@ -68,7 +68,7 @@ spec:
 			expectedOut: `apiVersion: v1
 kind: Pod
 metadata:
-  labels:
+  annotations:
     skaffold.dev/deployer: kubectl
   name: my-pod-123
   namespace: default
@@ -105,7 +105,7 @@ spec:
 			expectedOut: `apiVersion: v1
 kind: Pod
 metadata:
-  labels:
+  annotations:
     skaffold.dev/deployer: kubectl
   name: my-pod-123
   namespace: default
@@ -150,7 +150,7 @@ spec:
 			expectedOut: `apiVersion: v1
 kind: Pod
 metadata:
-  labels:
+  annotations:
     skaffold.dev/deployer: kubectl
   name: my-pod-123
   namespace: default
@@ -162,7 +162,7 @@ spec:
 apiVersion: v1
 kind: Pod
 metadata:
-  labels:
+  annotations:
     skaffold.dev/deployer: kubectl
   name: my-pod-456
   namespace: default
@@ -528,14 +528,15 @@ spec:
 			expectedOut: `apiVersion: v1
 kind: Pod
 metadata:
-  labels:
-    app.kubernetes.io/managed-by: SOMEDYNAMICVALUE
+  annotations:
     skaffold.dev/builder: local
     skaffold.dev/cleanup: "true"
     skaffold.dev/deployer: kubectl
     skaffold.dev/docker-api-version: SOMEDYNAMICVALUE
-    skaffold.dev/run-id: SOMEDYNAMICVALUE
     skaffold.dev/tag-policy: git-commit
+  labels:
+    app.kubernetes.io/managed-by: SOMEDYNAMICVALUE
+    skaffold.dev/run-id: SOMEDYNAMICVALUE
   name: my-pod-123
 spec:
   containers:
@@ -636,14 +637,15 @@ resources:
 			expectedOut: `apiVersion: v1
 kind: Pod
 metadata:
-  labels:
-    app.kubernetes.io/managed-by: SOMEDYNAMICVALUE
+  annotations:
     skaffold.dev/builder: local
     skaffold.dev/cleanup: "true"
     skaffold.dev/deployer: kustomize
     skaffold.dev/docker-api-version: SOMEDYNAMICVALUE
-    skaffold.dev/run-id: SOMEDYNAMICVALUE
     skaffold.dev/tag-policy: git-commit
+  labels:
+    app.kubernetes.io/managed-by: SOMEDYNAMICVALUE
+    skaffold.dev/run-id: SOMEDYNAMICVALUE
     this-is-from: kustomization.yaml
   name: my-pod-123
 spec:
diff --git a/pkg/skaffold/build/build.go b/pkg/skaffold/build/build.go
index 75d00909a10..1f433070235 100644
--- a/pkg/skaffold/build/build.go
+++ b/pkg/skaffold/build/build.go
@@ -37,6 +37,8 @@ type Artifact struct {
 type Builder interface {
 	Labels() map[string]string
 
+	Annotations() map[string]string
+
 	Build(ctx context.Context, out io.Writer, tags tag.ImageTags, artifacts []*latest.Artifact) ([]Artifact, error)
 
 	// Prune removes images built with Skaffold
diff --git a/pkg/skaffold/build/cluster/types.go b/pkg/skaffold/build/cluster/types.go
index 8a4a4a4f319..623f4b58991 100644
--- a/pkg/skaffold/build/cluster/types.go
+++ b/pkg/skaffold/build/cluster/types.go
@@ -56,6 +56,10 @@ func NewBuilder(runCtx *runcontext.RunContext) (*Builder, error) {
 
 // Labels are labels specific to cluster builder.
 func (b *Builder) Labels() map[string]string {
+	return map[string]string{}
+}
+
+func (b *Builder) Annotations() map[string]string {
 	return map[string]string{
 		constants.Labels.Builder: "cluster",
 	}
diff --git a/pkg/skaffold/build/cluster/types_test.go b/pkg/skaffold/build/cluster/types_test.go
index 3372317f5f9..a86f0c6bdb0 100644
--- a/pkg/skaffold/build/cluster/types_test.go
+++ b/pkg/skaffold/build/cluster/types_test.go
@@ -106,7 +106,8 @@ func TestNewBuilder(t *testing.T) {
 }
 
 func TestLabels(t *testing.T) {
-	testutil.CheckDeepEqual(t, map[string]string{"skaffold.dev/builder": "cluster"}, (&Builder{}).Labels())
+	testutil.CheckDeepEqual(t, map[string]string{}, (&Builder{}).Labels())
+	testutil.CheckDeepEqual(t, map[string]string{"skaffold.dev/builder": "cluster"}, (&Builder{}).Annotations())
 }
 
 func TestPruneIsNoop(t *testing.T) {
diff --git a/pkg/skaffold/build/gcb/types.go b/pkg/skaffold/build/gcb/types.go
index 7da63fe4a40..20c7aa48c6f 100644
--- a/pkg/skaffold/build/gcb/types.go
+++ b/pkg/skaffold/build/gcb/types.go
@@ -93,6 +93,10 @@ func NewBuilder(runCtx *runcontext.RunContext) *Builder {
 
 // Labels are labels specific to Google Cloud Build.
 func (b *Builder) Labels() map[string]string {
+	return map[string]string{}
+}
+
+func (b *Builder) Annotations() map[string]string {
 	return map[string]string{
 		constants.Labels.Builder: "google-cloud-build",
 	}
diff --git a/pkg/skaffold/build/local/types.go b/pkg/skaffold/build/local/types.go
index 4b32ad55c6d..dd071b5c0ce 100644
--- a/pkg/skaffold/build/local/types.go
+++ b/pkg/skaffold/build/local/types.go
@@ -95,6 +95,10 @@ func (b *Builder) PushImages() bool {
 
 // Labels are labels specific to local builder.
 func (b *Builder) Labels() map[string]string {
+	return map[string]string{}
+}
+
+func (b *Builder) Annotations() map[string]string {
 	labels := map[string]string{
 		constants.Labels.Builder: "local",
 	}
diff --git a/pkg/skaffold/build/tag/custom.go b/pkg/skaffold/build/tag/custom.go
index dcf8e515859..5626fccf566 100644
--- a/pkg/skaffold/build/tag/custom.go
+++ b/pkg/skaffold/build/tag/custom.go
@@ -28,6 +28,10 @@ type CustomTag struct {
 }
 
 func (c *CustomTag) Labels() map[string]string {
+	return map[string]string{}
+}
+
+func (c *CustomTag) Annotations() map[string]string {
 	return map[string]string{
 		constants.Labels.TagPolicy: "custom",
 	}
diff --git a/pkg/skaffold/build/tag/date_time.go b/pkg/skaffold/build/tag/date_time.go
index 064b33ccfc1..ceae17f7a45 100644
--- a/pkg/skaffold/build/tag/date_time.go
+++ b/pkg/skaffold/build/tag/date_time.go
@@ -45,6 +45,10 @@ func NewDateTimeTagger(format, timezone string) Tagger {
 }
 
 func (tagger *dateTimeTagger) Labels() map[string]string {
+	return map[string]string{}
+}
+
+func (tagger *dateTimeTagger) Annotations() map[string]string {
 	return map[string]string{
 		constants.Labels.TagPolicy: "dateTimeTagger",
 	}
diff --git a/pkg/skaffold/build/tag/env_template.go b/pkg/skaffold/build/tag/env_template.go
index 083bbbc9619..1aa0941a30d 100644
--- a/pkg/skaffold/build/tag/env_template.go
+++ b/pkg/skaffold/build/tag/env_template.go
@@ -44,6 +44,10 @@ func NewEnvTemplateTagger(t string) (Tagger, error) {
 }
 
 func (t *envTemplateTagger) Labels() map[string]string {
+	return map[string]string{}
+}
+
+func (t *envTemplateTagger) Annotations() map[string]string {
 	return map[string]string{
 		constants.Labels.TagPolicy: "envTemplateTagger",
 	}
diff --git a/pkg/skaffold/build/tag/git_commit.go b/pkg/skaffold/build/tag/git_commit.go
index d4ddf0407ed..51e8f0f3e9a 100644
--- a/pkg/skaffold/build/tag/git_commit.go
+++ b/pkg/skaffold/build/tag/git_commit.go
@@ -60,6 +60,11 @@ func NewGitCommit(prefix, variant string) (*GitCommit, error) {
 
 // Labels are labels specific to the git tagger.
 func (c *GitCommit) Labels() map[string]string {
+	return map[string]string{}
+}
+
+// Labels are labels specific to the git tagger.
+func (c *GitCommit) Annotations() map[string]string {
 	return map[string]string{
 		constants.Labels.TagPolicy: "git-commit",
 	}
diff --git a/pkg/skaffold/build/tag/sha256.go b/pkg/skaffold/build/tag/sha256.go
index c0b4e4f4115..34084cd7729 100644
--- a/pkg/skaffold/build/tag/sha256.go
+++ b/pkg/skaffold/build/tag/sha256.go
@@ -26,6 +26,11 @@ type ChecksumTagger struct{}
 
 // Labels are labels specific to the sha256 tagger.
 func (c *ChecksumTagger) Labels() map[string]string {
+	return map[string]string{}
+}
+
+// Labels are labels specific to the sha256 tagger.
+func (c *ChecksumTagger) Annotations() map[string]string {
 	return map[string]string{
 		constants.Labels.TagPolicy: "sha256",
 	}
diff --git a/pkg/skaffold/build/tag/tag.go b/pkg/skaffold/build/tag/tag.go
index 879898a0772..b57da44cb3d 100644
--- a/pkg/skaffold/build/tag/tag.go
+++ b/pkg/skaffold/build/tag/tag.go
@@ -24,6 +24,8 @@ type Tagger interface {
 	// Labels produces labels to indicate the used tagger in deployed pods.
 	Labels() map[string]string
 
+	Annotations() map[string]string
+
 	// GenerateFullyQualifiedImageName resolves the fully qualified image name for an artifact.
 	// The workingDir is the root directory of the artifact with respect to the Skaffold root,
 	// and imageName is the base name of the image.
diff --git a/pkg/skaffold/deploy/helm.go b/pkg/skaffold/deploy/helm.go
index 57b362ee3e3..ff58237925e 100644
--- a/pkg/skaffold/deploy/helm.go
+++ b/pkg/skaffold/deploy/helm.go
@@ -92,6 +92,10 @@ func NewHelmDeployer(runCtx *runcontext.RunContext) *HelmDeployer {
 
 // Labels returns the Kubernetes labels used by this deployer
 func (h *HelmDeployer) Labels() map[string]string {
+	return map[string]string{}
+}
+
+func (h *HelmDeployer) Annotations() map[string]string {
 	return map[string]string{
 		constants.Labels.Deployer: "helm",
 	}
@@ -143,8 +147,8 @@ func (h *HelmDeployer) Deploy(ctx context.Context, out io.Writer, builds []build
 
 	event.DeployComplete()
 
-	labels := merge(h.addSkaffoldLabels, h, labellers...)
-	labelDeployResults(labels, dRes)
+	labels, annotations := merge(h.addSkaffoldLabels, h, labellers...)
+	labelAndAnnotateDeployResults(labels, annotations, dRes)
 
 	// Collect namespaces in a string
 	namespaces := make([]string, 0, len(nsMap))
diff --git a/pkg/skaffold/deploy/kubectl.go b/pkg/skaffold/deploy/kubectl.go
index 34aa10cfed0..dc79868a708 100644
--- a/pkg/skaffold/deploy/kubectl.go
+++ b/pkg/skaffold/deploy/kubectl.go
@@ -76,6 +76,10 @@ func NewKubectlDeployer(runCtx *runcontext.RunContext) *KubectlDeployer {
 }
 
 func (k *KubectlDeployer) Labels() map[string]string {
+	return map[string]string{}
+}
+
+func (k *KubectlDeployer) Annotations() map[string]string {
 	return map[string]string{
 		constants.Labels.Deployer: "kubectl",
 	}
@@ -298,7 +302,7 @@ func (k *KubectlDeployer) renderManifests(ctx context.Context, out io.Writer, bu
 		}
 	}
 
-	manifests, err = manifests.SetLabels(merge(k.addSkaffoldLabels, k, labellers...))
+	manifests, err = manifests.SetLabelsAndAnnotations(merge(k.addSkaffoldLabels, k, labellers...))
 	if err != nil {
 		return nil, fmt.Errorf("setting labels in manifests: %w", err)
 	}
diff --git a/pkg/skaffold/deploy/kubectl/labels.go b/pkg/skaffold/deploy/kubectl/labels.go
index 8ef369780ec..fa4a8924b57 100644
--- a/pkg/skaffold/deploy/kubectl/labels.go
+++ b/pkg/skaffold/deploy/kubectl/labels.go
@@ -23,8 +23,8 @@ import (
 )
 
 // SetLabels add labels to a list of Kubernetes manifests.
-func (l *ManifestList) SetLabels(labels map[string]string) (ManifestList, error) {
-	replacer := newLabelsSetter(labels)
+func (l *ManifestList) SetLabelsAndAnnotations(labels, annotations map[string]string) (ManifestList, error) {
+	replacer := newLabelsAndAnnotationsSetter(labels, annotations)
 
 	updated, err := l.Visit(replacer)
 	if err != nil {
@@ -36,45 +36,54 @@ func (l *ManifestList) SetLabels(labels map[string]string) (ManifestList, error)
 	return updated, nil
 }
 
-type labelsSetter struct {
-	labels map[string]string
+type labelsAndAnnotationsSetter struct {
+	labels      map[string]string
+	annotations map[string]string
 }
 
-func newLabelsSetter(labels map[string]string) *labelsSetter {
-	return &labelsSetter{
-		labels: labels,
+func newLabelsAndAnnotationsSetter(labels, annotations map[string]string) *labelsAndAnnotationsSetter {
+	return &labelsAndAnnotationsSetter{
+		labels:      labels,
+		annotations: annotations,
 	}
 }
 
-func (r *labelsSetter) Visit(o map[string]interface{}, k string, v interface{}) bool {
+func (r *labelsAndAnnotationsSetter) Visit(o map[string]interface{}, k string, v interface{}) bool {
 	if k != "metadata" {
 		return true
 	}
 
-	if len(r.labels) == 0 {
-		return false
-	}
-
 	metadata, ok := v.(map[string]interface{})
 	if !ok {
 		return true
 	}
 
-	l, present := metadata["labels"]
+	if visitAndReplace("labels", r.labels, &metadata) {
+		return true
+	}
+	return visitAndReplace("annotations", r.annotations, &metadata)
+}
+
+func visitAndReplace(fieldName string, values map[string]string, metadata *map[string]interface{}) bool {
+	if len(values) == 0 {
+		return false
+	}
+
+	field, present := (*metadata)[fieldName]
 	if !present {
-		metadata["labels"] = r.labels
+		(*metadata)[fieldName] = values
 		return false
 	}
 
-	labels, ok := l.(map[string]interface{})
+	existingValues, ok := field.(map[string]interface{})
 	if !ok {
 		return true
 	}
 
-	for k, v := range r.labels {
-		// Don't replace existing label.
-		if _, present := labels[k]; !present {
-			labels[k] = v
+	for k, v := range values {
+		// Don't overwrite existing values
+		if _, present := existingValues[k]; !present {
+			existingValues[k] = v
 		}
 	}
 
diff --git a/pkg/skaffold/deploy/kubectl/labels_test.go b/pkg/skaffold/deploy/kubectl/labels_test.go
index b62b116652c..475b3e20369 100644
--- a/pkg/skaffold/deploy/kubectl/labels_test.go
+++ b/pkg/skaffold/deploy/kubectl/labels_test.go
@@ -22,7 +22,7 @@ import (
 	"github.com/GoogleContainerTools/skaffold/testutil"
 )
 
-func TestSetLabels(t *testing.T) {
+func TestSetLabelsAndAnnotations(t *testing.T) {
 	manifests := ManifestList{[]byte(`
 apiVersion: v1
 kind: Pod
@@ -38,6 +38,9 @@ spec:
 apiVersion: v1
 kind: Pod
 metadata:
+  annotations:
+    key1: value1
+    key2: value2
   labels:
     key1: value1
     key2: value2
@@ -48,7 +51,10 @@ spec:
     name: example
 `)}
 
-	resultManifest, err := manifests.SetLabels(map[string]string{
+	resultManifest, err := manifests.SetLabelsAndAnnotations(map[string]string{
+		"key1": "value1",
+		"key2": "value2",
+	}, map[string]string{
 		"key1": "value1",
 		"key2": "value2",
 	})
@@ -56,11 +62,13 @@ spec:
 	testutil.CheckErrorAndDeepEqual(t, false, err, expected.String(), resultManifest.String())
 }
 
-func TestAddLabels(t *testing.T) {
+func TestAddLabelsAndAnnotations(t *testing.T) {
 	manifests := ManifestList{[]byte(`
 apiVersion: v1
 kind: Pod
 metadata:
+  annotations:
+    key0: value0
   labels:
     key0: value0
   name: getting-started
@@ -74,6 +82,10 @@ spec:
 apiVersion: v1
 kind: Pod
 metadata:
+  annotations:
+    key0: value0
+    key1: value1
+    key2: value2
   labels:
     key0: value0
     key1: value1
@@ -85,7 +97,11 @@ spec:
     name: example
 `)}
 
-	resultManifest, err := manifests.SetLabels(map[string]string{
+	resultManifest, err := manifests.SetLabelsAndAnnotations(map[string]string{
+		"key0": "should-be-ignored",
+		"key1": "value1",
+		"key2": "value2",
+	}, map[string]string{
 		"key0": "should-be-ignored",
 		"key1": "value1",
 		"key2": "value2",
@@ -94,7 +110,7 @@ spec:
 	testutil.CheckErrorAndDeepEqual(t, false, err, expected.String(), resultManifest.String())
 }
 
-func TestSetNoLabel(t *testing.T) {
+func TestSetNoLabelOrAnnotation(t *testing.T) {
 	manifests := ManifestList{[]byte(`
 apiVersion: v1
 kind: Pod
@@ -117,12 +133,12 @@ spec:
     name: example
 `)}
 
-	resultManifest, err := manifests.SetLabels(nil)
+	resultManifest, err := manifests.SetLabelsAndAnnotations(nil, nil)
 
 	testutil.CheckErrorAndDeepEqual(t, false, err, expected.String(), resultManifest.String())
 }
 
-func TestSetNoLabelWhenTypeUnexpected(t *testing.T) {
+func TestSetNoLabelOrAnnotationWhenTypeUnexpected(t *testing.T) {
 	manifests := ManifestList{[]byte(`
 apiVersion: v1
 kind: Pod
@@ -132,16 +148,17 @@ metadata: 3
 apiVersion: v1
 kind: Pod
 metadata:
+  annotations: 3
   labels: 3
   name: getting-started
 `)}
 
-	resultManifest, err := manifests.SetLabels(map[string]string{"key0": "value0"})
+	resultManifest, err := manifests.SetLabelsAndAnnotations(map[string]string{"key0": "value0"}, map[string]string{"key0": "value0"})
 
 	testutil.CheckErrorAndDeepEqual(t, false, err, manifests.String(), resultManifest.String())
 }
 
-func TestSetNoLabelInCRDSchema(t *testing.T) {
+func TestSetLabelAndAnnotationInCRDSchema(t *testing.T) {
 	manifests := ManifestList{[]byte(`apiVersion: apiextensions.k8s.io/v1beta1
 kind: CustomResourceDefinition
 metadata:
@@ -163,6 +180,9 @@ spec:
 	expected := ManifestList{[]byte(`apiVersion: apiextensions.k8s.io/v1beta1
 kind: CustomResourceDefinition
 metadata:
+  annotations:
+    key0: value0
+    key1: value1
   labels:
     key0: value0
     key1: value1
@@ -181,7 +201,10 @@ spec:
         metadata:
           type: object`)}
 
-	resultManifest, err := manifests.SetLabels(map[string]string{
+	resultManifest, err := manifests.SetLabelsAndAnnotations(map[string]string{
+		"key0": "value0",
+		"key1": "value1",
+	}, map[string]string{
 		"key0": "value0",
 		"key1": "value1",
 	})
diff --git a/pkg/skaffold/deploy/kubectl_test.go b/pkg/skaffold/deploy/kubectl_test.go
index 84c920a23b5..adadbb7c9b7 100644
--- a/pkg/skaffold/deploy/kubectl_test.go
+++ b/pkg/skaffold/deploy/kubectl_test.go
@@ -363,7 +363,7 @@ func TestKubectlRedeploy(t *testing.T) {
 			AndRunInput("kubectl --context kubecontext --namespace testNamespace apply -f -", `apiVersion: v1
 kind: Pod
 metadata:
-  labels:
+  annotations:
     skaffold.dev/deployer: kubectl
   name: leeroy-app
 spec:
@@ -374,7 +374,7 @@ spec:
 apiVersion: v1
 kind: Pod
 metadata:
-  labels:
+  annotations:
     skaffold.dev/deployer: kubectl
   name: leeroy-web
 spec:
@@ -385,7 +385,7 @@ spec:
 			AndRunInput("kubectl --context kubecontext --namespace testNamespace apply -f -", `apiVersion: v1
 kind: Pod
 metadata:
-  labels:
+  annotations:
     skaffold.dev/deployer: kubectl
   name: leeroy-app
 spec:
@@ -535,7 +535,7 @@ spec:
 			expected: `apiVersion: v1
 kind: Pod
 metadata:
-  labels:
+  annotations:
     skaffold.dev/deployer: kubectl
   namespace: default
 spec:
@@ -570,7 +570,7 @@ spec:
 			expected: `apiVersion: v1
 kind: Pod
 metadata:
-  labels:
+  annotations:
     skaffold.dev/deployer: kubectl
   namespace: default
 spec:
@@ -598,7 +598,7 @@ spec:
 			expected: `apiVersion: v1
 kind: Pod
 metadata:
-  labels:
+  annotations:
     skaffold.dev/deployer: kubectl
   namespace: default
 spec:
diff --git a/pkg/skaffold/deploy/kustomize.go b/pkg/skaffold/deploy/kustomize.go
index 6f5d03ea30e..5a8f3615d0f 100644
--- a/pkg/skaffold/deploy/kustomize.go
+++ b/pkg/skaffold/deploy/kustomize.go
@@ -119,6 +119,10 @@ func NewKustomizeDeployer(runCtx *runcontext.RunContext) *KustomizeDeployer {
 
 // Labels returns the labels specific to kustomize.
 func (k *KustomizeDeployer) Labels() map[string]string {
+	return map[string]string{}
+}
+
+func (k *KustomizeDeployer) Annotations() map[string]string {
 	return map[string]string{
 		constants.Labels.Deployer: "kustomize",
 	}
@@ -186,7 +190,7 @@ func (k *KustomizeDeployer) renderManifests(ctx context.Context, out io.Writer,
 		}
 	}
 
-	manifests, err = manifests.SetLabels(merge(k.addSkaffoldLabels, k, labellers...))
+	manifests, err = manifests.SetLabelsAndAnnotations(merge(k.addSkaffoldLabels, k, labellers...))
 	if err != nil {
 		return nil, fmt.Errorf("setting labels in manifests: %w", err)
 	}
diff --git a/pkg/skaffold/deploy/kustomize_test.go b/pkg/skaffold/deploy/kustomize_test.go
index 5c51eb31281..a0e67311afc 100644
--- a/pkg/skaffold/deploy/kustomize_test.go
+++ b/pkg/skaffold/deploy/kustomize_test.go
@@ -470,12 +470,18 @@ func TestKustomizeBuildCommandArgs(t *testing.T) {
 }
 
 type testLabels struct {
-	labels map[string]string
+	labels      map[string]string
+	annotations map[string]string
 }
 
 func (t *testLabels) Labels() map[string]string {
 	return t.labels
 }
+
+func (t *testLabels) Annotations() map[string]string {
+	return t.annotations
+}
+
 func TestKustomizeRender(t *testing.T) {
 	type kustomizationCall struct {
 		folder      string
@@ -520,7 +526,7 @@ spec:
 			expected: `apiVersion: v1
 kind: Pod
 metadata:
-  labels:
+  annotations:
     skaffold.dev/deployer: kustomize
   namespace: default
 spec:
@@ -568,8 +574,9 @@ spec:
 			expected: `apiVersion: v1
 kind: Pod
 metadata:
-  labels:
+  annotations:
     skaffold.dev/deployer: kustomize
+  labels:
     user/label: test
   namespace: default
 spec:
@@ -621,7 +628,7 @@ spec:
 			expected: `apiVersion: v1
 kind: Pod
 metadata:
-  labels:
+  annotations:
     skaffold.dev/deployer: kustomize
   namespace: default
 spec:
@@ -632,7 +639,7 @@ spec:
 apiVersion: v1
 kind: Pod
 metadata:
-  labels:
+  annotations:
     skaffold.dev/deployer: kustomize
   namespace: default
 spec:
diff --git a/pkg/skaffold/deploy/labeller.go b/pkg/skaffold/deploy/labeller.go
index 9c71bf2dfbf..9f559101bee 100644
--- a/pkg/skaffold/deploy/labeller.go
+++ b/pkg/skaffold/deploy/labeller.go
@@ -56,23 +56,10 @@ func NewLabeller(opts config.SkaffoldOptions) *DefaultLabeller {
 
 func (d *DefaultLabeller) Labels() map[string]string {
 	labels := map[string]string{
-		K8sManagedByLabelKey: fmt.Sprintf("skaffold-%s", d.version),
+		K8sManagedByLabelKey: "skaffold",
 		RunIDLabel:           d.runID,
 	}
 
-	if d.opts.Cleanup {
-		labels["skaffold.dev/cleanup"] = "true"
-	}
-	if d.opts.Tail {
-		labels["skaffold.dev/tail"] = "true"
-	}
-	if d.opts.Namespace != "" {
-		labels["skaffold.dev/namespace"] = d.opts.Namespace
-	}
-	for i, profile := range d.opts.Profiles {
-		key := fmt.Sprintf("skaffold.dev/profile.%d", i)
-		labels[key] = profile
-	}
 	for _, cl := range d.opts.CustomLabels {
 		l := strings.SplitN(cl, "=", 2)
 		if len(l) == 1 {
@@ -84,6 +71,25 @@ func (d *DefaultLabeller) Labels() map[string]string {
 	return labels
 }
 
+func (d *DefaultLabeller) Annotations() map[string]string {
+	annotations := map[string]string{}
+
+	if d.opts.Cleanup {
+		annotations["skaffold.dev/cleanup"] = "true"
+	}
+	if d.opts.Tail {
+		annotations["skaffold.dev/tail"] = "true"
+	}
+	if d.opts.Namespace != "" {
+		annotations["skaffold.dev/namespace"] = d.opts.Namespace
+	}
+	for i, profile := range d.opts.Profiles {
+		key := fmt.Sprintf("skaffold.dev/profile.%d", i)
+		annotations[key] = profile
+	}
+	return annotations
+}
+
 func (d *DefaultLabeller) RunIDSelector() string {
 	return fmt.Sprintf("%s=%s", RunIDLabel, d.Labels()[RunIDLabel])
 }
diff --git a/pkg/skaffold/deploy/labels.go b/pkg/skaffold/deploy/labels.go
index d2cd3b9a945..9a09c7e1e13 100644
--- a/pkg/skaffold/deploy/labels.go
+++ b/pkg/skaffold/deploy/labels.go
@@ -41,25 +41,32 @@ type Artifact struct {
 	Namespace string
 }
 
-// Labeller can give key/value labels to set on deployed resources.
+// Labeller can give key/value labels and annotations to set on deployed resources.
 type Labeller interface {
 	// Labels keys must be prefixed with "skaffold.dev/"
 	Labels() map[string]string
+
+	Annotations() map[string]string
 }
 
 // merge merges the labels from multiple sources.
-func merge(addSkaffoldLabels bool, deployer Labeller, sources ...Labeller) map[string]string {
+func merge(addSkaffoldLabels bool, deployer Labeller, sources ...Labeller) (map[string]string, map[string]string) {
 	if !addSkaffoldLabels {
-		return map[string]string{}
+		return map[string]string{}, map[string]string{}
 	}
 
-	merged := deployer.Labels()
+	mergedLabels := deployer.Labels()
 
 	for _, src := range sources {
-		copyMap(merged, src.Labels())
+		copyMap(mergedLabels, src.Labels())
 	}
 
-	return merged
+	mergedAnnotations := deployer.Annotations()
+	for _, src := range sources {
+		copyMap(mergedAnnotations, src.Annotations())
+	}
+
+	return mergedLabels, mergedAnnotations
 }
 
 // retry 3 times to give the object time to propagate to the API server
@@ -68,7 +75,7 @@ const (
 	sleeptime = 300 * time.Millisecond
 )
 
-func labelDeployResults(labels map[string]string, results []Artifact) {
+func labelAndAnnotateDeployResults(labels, annotations map[string]string, results []Artifact) {
 	// use the kubectl client to update all k8s objects with a skaffold watermark
 	dynClient, err := kubernetes.DynamicClient()
 	if err != nil {
@@ -85,7 +92,7 @@ func labelDeployResults(labels map[string]string, results []Artifact) {
 	for _, res := range results {
 		err = nil
 		for i := 0; i < tries; i++ {
-			if err = updateRuntimeObject(dynClient, client.Discovery(), labels, res); err == nil {
+			if err = updateRuntimeObject(dynClient, client.Discovery(), labels, annotations, res); err == nil {
 				break
 			}
 			time.Sleep(sleeptime)
@@ -105,7 +112,16 @@ func addLabels(labels map[string]string, accessor metav1.Object) {
 	accessor.SetLabels(kv)
 }
 
-func updateRuntimeObject(client dynamic.Interface, disco discovery.DiscoveryInterface, labels map[string]string, res Artifact) error {
+func addAnnotations(annotations map[string]string, accessor metav1.Object) {
+	kv := make(map[string]string)
+
+	copyMap(kv, annotations)
+	copyMap(kv, accessor.GetAnnotations())
+
+	accessor.SetAnnotations(kv)
+}
+
+func updateRuntimeObject(client dynamic.Interface, disco discovery.DiscoveryInterface, labels, annotations map[string]string, res Artifact) error {
 	originalJSON, _ := json.Marshal(res.Obj)
 	modifiedObj := res.Obj.DeepCopyObject()
 	accessor, err := meta.Accessor(modifiedObj)
@@ -115,6 +131,7 @@ func updateRuntimeObject(client dynamic.Interface, disco discovery.DiscoveryInte
 	name := accessor.GetName()
 
 	addLabels(labels, accessor)
+	addAnnotations(annotations, accessor)
 
 	modifiedJSON, _ := json.Marshal(modifiedObj)
 	p, _ := patch.CreateTwoWayMergePatch(originalJSON, modifiedJSON, modifiedObj)
diff --git a/pkg/skaffold/deploy/labels_test.go b/pkg/skaffold/deploy/labels_test.go
index 756d6c1c0a4..bb41da7f15e 100644
--- a/pkg/skaffold/deploy/labels_test.go
+++ b/pkg/skaffold/deploy/labels_test.go
@@ -50,6 +50,10 @@ func TestLabelDeployResults(t *testing.T) {
 		existingLabels map[string]string
 		appliedLabels  map[string]string
 		expectedLabels map[string]string
+
+		existingAnnotations map[string]string
+		appliedAnnotations  map[string]string
+		expectedAnnotations map[string]string
 	}{
 		{
 			description:    "set labels",
@@ -77,6 +81,32 @@ func TestLabelDeployResults(t *testing.T) {
 				"key1": "value1",
 			},
 		},
+		{
+			description:         "set annotations",
+			existingAnnotations: map[string]string{},
+			appliedAnnotations: map[string]string{
+				"key1": "value1",
+				"key2": "value2",
+			},
+			expectedAnnotations: map[string]string{
+				"key1": "value1",
+				"key2": "value2",
+			},
+		},
+		{
+			description: "add annotations",
+			existingAnnotations: map[string]string{
+				"key0": "value0",
+			},
+			appliedAnnotations: map[string]string{
+				"key0": "should-be-ignored",
+				"key1": "value1",
+			},
+			expectedAnnotations: map[string]string{
+				"key0": "value0",
+				"key1": "value1",
+			},
+		},
 	}
 
 	for _, test := range tests {
@@ -87,8 +117,9 @@ func TestLabelDeployResults(t *testing.T) {
 					Kind:       "Deployment",
 				},
 				ObjectMeta: metav1.ObjectMeta{
-					Name:   "foo",
-					Labels: test.existingLabels,
+					Name:        "foo",
+					Labels:      test.existingLabels,
+					Annotations: test.existingAnnotations,
 				},
 			}
 
@@ -106,12 +137,13 @@ func TestLabelDeployResults(t *testing.T) {
 			t.Override(&k8s.DynamicClient, mockDynamicClient(dynClient))
 
 			// Patch labels
-			labelDeployResults(test.appliedLabels, []Artifact{{Obj: dep}})
+			labelAndAnnotateDeployResults(test.appliedLabels, test.appliedAnnotations, []Artifact{{Obj: dep}})
 
 			// Check modified value
 			modified, err := dynClient.Resource(schema.GroupVersionResource{Group: "apps", Version: "v1", Resource: "deployments"}).Get("foo", metav1.GetOptions{})
 			t.CheckNoError(err)
 			t.CheckDeepEqual(test.expectedLabels, modified.GetLabels())
+			t.CheckDeepEqual(test.expectedAnnotations, modified.GetAnnotations())
 		})
 	}
 }
diff --git a/pkg/skaffold/runner/runner_test.go b/pkg/skaffold/runner/runner_test.go
index a77ec54d3fd..ce454e853bb 100644
--- a/pkg/skaffold/runner/runner_test.go
+++ b/pkg/skaffold/runner/runner_test.go
@@ -91,6 +91,7 @@ func (t *TestBench) WithTestErrors(testErrors []error) *TestBench {
 }
 
 func (t *TestBench) Labels() map[string]string                        { return map[string]string{} }
+func (t *TestBench) Annotations() map[string]string                   { return map[string]string{} }
 func (t *TestBench) TestDependencies() ([]string, error)              { return nil, nil }
 func (t *TestBench) Dependencies() ([]string, error)                  { return nil, nil }
 func (t *TestBench) Cleanup(ctx context.Context, out io.Writer) error { return nil }
diff --git a/pkg/skaffold/sync/sync_test.go b/pkg/skaffold/sync/sync_test.go
index 449804a334a..2e41b5a650f 100644
--- a/pkg/skaffold/sync/sync_test.go
+++ b/pkg/skaffold/sync/sync_test.go
@@ -862,7 +862,7 @@ var pod = &v1.Pod{
 	ObjectMeta: metav1.ObjectMeta{
 		Name: "podname",
 		Labels: map[string]string{
-			"app.kubernetes.io/managed-by": "skaffold-dirty",
+			"app.kubernetes.io/managed-by": "skaffold",
 		},
 	},
 	Status: v1.PodStatus{
@@ -882,7 +882,7 @@ var nonRunningPod = &v1.Pod{
 	ObjectMeta: metav1.ObjectMeta{
 		Name: "podname",
 		Labels: map[string]string{
-			"app.kubernetes.io/managed-by": "skaffold-dirty",
+			"app.kubernetes.io/managed-by": "skaffold",
 		},
 	},
 	Status: v1.PodStatus{