diff --git a/kyaml/kio/byteio_writer.go b/kyaml/kio/byteio_writer.go
index c6fe96db4..84097f108 100644
--- a/kyaml/kio/byteio_writer.go
+++ b/kyaml/kio/byteio_writer.go
@@ -72,15 +72,8 @@ func (w ByteWriter) Write(nodes []*yaml.RNode) error {
 			}
 		}
 
-		// TODO(pwittrock): factor this into a a common module for pruning empty values
-		_, err := nodes[i].Pipe(yaml.Lookup("metadata"), yaml.FieldClearer{
-			Name: "annotations", IfEmpty: true})
-		if err != nil {
-			return errors.Wrap(err)
-		}
-		_, err = nodes[i].Pipe(yaml.FieldClearer{Name: "metadata", IfEmpty: true})
-		if err != nil {
-			return errors.Wrap(err)
+		if err := yaml.ClearEmptyAnnotations(nodes[i]); err != nil {
+			return err
 		}
 
 		if w.Style != 0 {
diff --git a/kyaml/kio/pkgio_reader_test.go b/kyaml/kio/pkgio_reader_test.go
index 62810277d..7f68fdd73 100644
--- a/kyaml/kio/pkgio_reader_test.go
+++ b/kyaml/kio/pkgio_reader_test.go
@@ -71,6 +71,17 @@ g:
   - j
 `)
 
+var readFileC = []byte(`---
+a: b #third
+metadata:
+  annotations:
+`)
+
+var readFileD = []byte(`---
+a: b #forth
+metadata:
+`)
+
 var pkgFile = []byte(``)
 
 func TestLocalPackageReader_Read_empty(t *testing.T) {
@@ -87,6 +98,8 @@ func TestLocalPackageReader_Read_pkg(t *testing.T) {
 	defer s.clean()
 	s.writeFile(t, filepath.Join("a_test.yaml"), readFileA)
 	s.writeFile(t, filepath.Join("b_test.yaml"), readFileB)
+	s.writeFile(t, filepath.Join("c_test.yaml"), readFileC)
+	s.writeFile(t, filepath.Join("d_test.yaml"), readFileD)
 
 	paths := []struct {
 		path string
@@ -101,7 +114,7 @@ func TestLocalPackageReader_Read_pkg(t *testing.T) {
 			return
 		}
 
-		if !assert.Len(t, nodes, 3) {
+		if !assert.Len(t, nodes, 5) {
 			return
 		}
 		expected := []string{
@@ -127,6 +140,18 @@ metadata:
   annotations:
     config.kubernetes.io/index: '0'
     config.kubernetes.io/path: 'b_test.yaml'
+`,
+			`a: b #third
+metadata:
+  annotations:
+    config.kubernetes.io/index: '0'
+    config.kubernetes.io/path: 'c_test.yaml'
+`,
+			`a: b #forth
+metadata:
+  annotations:
+    config.kubernetes.io/index: '0'
+    config.kubernetes.io/path: 'd_test.yaml'
 `,
 		}
 		for i := range nodes {
diff --git a/kyaml/yaml/kfns.go b/kyaml/yaml/kfns.go
index 229c9c4ca..a8545e41b 100644
--- a/kyaml/yaml/kfns.go
+++ b/kyaml/yaml/kfns.go
@@ -5,6 +5,7 @@ package yaml
 
 import (
 	"gopkg.in/yaml.v3"
+	"sigs.k8s.io/kustomize/kyaml/errors"
 )
 
 // AnnotationClearer removes an annotation at metadata.annotations.
@@ -24,6 +25,21 @@ func ClearAnnotation(key string) AnnotationClearer {
 	return AnnotationClearer{Key: key}
 }
 
+// ClearEmptyAnnotations clears the keys, annotations
+// and metadata if they are empty/null
+func ClearEmptyAnnotations(rn *RNode) error {
+	_, err := rn.Pipe(Lookup("metadata"), FieldClearer{
+		Name: "annotations", IfEmpty: true})
+	if err != nil {
+		return errors.Wrap(err)
+	}
+	_, err = rn.Pipe(FieldClearer{Name: "metadata", IfEmpty: true})
+	if err != nil {
+		return errors.Wrap(err)
+	}
+	return nil
+}
+
 // AnnotationSetter sets an annotation at metadata.annotations.
 // Creates metadata.annotations if does not exist.
 type AnnotationSetter struct {
@@ -37,6 +53,11 @@ func (s AnnotationSetter) Filter(rn *RNode) (*RNode, error) {
 	v := NewScalarRNode(s.Value)
 	v.YNode().Tag = StringTag
 	v.YNode().Style = yaml.SingleQuotedStyle
+
+	if err := ClearEmptyAnnotations(rn); err != nil {
+		return nil, err
+	}
+
 	return rn.Pipe(
 		PathGetter{Path: []string{"metadata", "annotations"}, Create: yaml.MappingNode},
 		FieldSetter{Name: s.Key, Value: v})