diff --git a/api/filters/annotations/example_test.go b/api/filters/annotations/example_test.go
index 270193496..75eb51314 100644
--- a/api/filters/annotations/example_test.go
+++ b/api/filters/annotations/example_test.go
@@ -28,7 +28,9 @@ metadata:
 `)}},
 		Filters: []kio.Filter{Filter{
 			Annotations: map[string]string{
-				"foo": "bar",
+				"foo":          "bar",
+				"booleanValue": "true",
+				"numberValue":  "42",
 			},
 			FsSlice: fss,
 		}},
@@ -44,12 +46,16 @@ metadata:
 	// metadata:
 	//   name: instance
 	//   annotations:
+	//     booleanValue: "true"
 	//     foo: bar
+	//     numberValue: "42"
 	// ---
 	// apiVersion: example.com/v1
 	// kind: Bar
 	// metadata:
 	//   name: instance
 	//   annotations:
+	//     booleanValue: "true"
 	//     foo: bar
+	//     numberValue: "42"
 }
diff --git a/api/krusty/basic_io_test.go b/api/krusty/basic_io_test.go
index 9700ec41a..1ed567605 100644
--- a/api/krusty/basic_io_test.go
+++ b/api/krusty/basic_io_test.go
@@ -4,7 +4,6 @@
 package krusty_test
 
 import (
-	"fmt"
 	"testing"
 
 	kusttest_test "sigs.k8s.io/kustomize/api/testutils/kusttest"
@@ -28,7 +27,8 @@ func TestBasicIO_1(t *testing.T) {
 		//     return an error (that is then ignored by GetAnnotations)
 		//   }
 		// The error happens when any annotation value can be interpreted as
-		// a boolean or number.
+		// a boolean or number.  Such annotations cannot be successfully applied
+		// to an object in a cluster unless they are quoted.
 		t.SkipNow()
 	}
 	th.WriteK(".", `
@@ -49,6 +49,7 @@ spec:
 `)
 	m := th.Run(".", opts)
 	// The annotations are sorted by key, hence the order change.
+	// Quotes are added intentionally.
 	th.AssertActualEqualsExpected(
 		m, `
 apiVersion: v1
@@ -56,8 +57,8 @@ kind: Service
 metadata:
   annotations:
     color: green
-    happy: true
-    port: 8080
+    happy: "true"
+    port: "8080"
   name: demo
 spec:
   clusterIP: None
@@ -71,9 +72,7 @@ func TestBasicIO_2(t *testing.T) {
 resources:
 - service.yaml
 `)
-	// All the annotation values are quoted.
-	// The apimachinery code path retains the quotes, the kyaml
-	// path drops them at the moment.
+	// All the annotation values are quoted in the input.
 	th.WriteF("service.yaml", `
 apiVersion: v1
 kind: Service
@@ -88,20 +87,16 @@ spec:
 `)
 	m := th.Run(".", opts)
 	// The annotations are sorted by key, hence the order change.
-	expFmt := `
+	th.AssertActualEqualsExpected(m, `
 apiVersion: v1
 kind: Service
 metadata:
   annotations:
     color: green
-    happy: %s
-    port: %s
+    happy: "true"
+    port: "8080"
   name: demo
 spec:
   clusterIP: None
-`
-	th.AssertActualEqualsExpected(
-		m, opts.IfApiMachineryElseKyaml(
-			fmt.Sprintf(expFmt, `"true"`, `"8080"`),
-			fmt.Sprintf(expFmt, `true`, `8080`)))
+`)
 }
diff --git a/api/krusty/fnplugin_test.go b/api/krusty/fnplugin_test.go
index 97aa4b153..b45316a23 100644
--- a/api/krusty/fnplugin_test.go
+++ b/api/krusty/fnplugin_test.go
@@ -1,7 +1,6 @@
 package krusty_test
 
 import (
-	"fmt"
 	"os/exec"
 	"testing"
 
@@ -129,9 +128,8 @@ stringData:
     bootcmd:
     - mkdir /mnt/vda
 `)
-	opts := th.MakeOptionsPluginsEnabled()
-	m := th.Run("/app", opts)
-	expFmt := `
+	m := th.Run("/app", th.MakeOptionsPluginsEnabled())
+	th.AssertActualEqualsExpected(m, `
 apiVersion: v1
 kind: Secret
 metadata:
@@ -154,7 +152,7 @@ metadata:
     name: demo
   name: demo-budget
 spec:
-  minAvailable: 67%%
+  minAvailable: 67%
   selector:
     matchLabels:
       app: cockroachdb
@@ -187,7 +185,9 @@ metadata:
   annotations:
     config.kubernetes.io/path: config/demo_service.yaml
     prometheus.io/path: _status/vars
-%s
+    prometheus.io/port: "8080"
+    prometheus.io/scrape: "true"
+    service.alpha.kubernetes.io/tolerate-unready-endpoints: "true"
   labels:
     app: cockroachdb
     name: demo
@@ -244,7 +244,7 @@ spec:
         - /bin/bash
         - -ecx
         - |
-          # The use of qualified ` + "`hostname -f`" + ` is crucial:
+          # The use of qualified `+"`hostname -f`"+` is crucial:
           # Other nodes aren't able to look up the unqualified hostname.
           CRARGS=("start" "--logtostderr" "--insecure" "--host" "$(hostname -f)" "--http-host" "0.0.0.0")
           # We only want to initialize a new cluster (by omitting the join flag)
@@ -302,14 +302,7 @@ spec:
       resources:
         requests:
           storage: 1Gi
-`
-	th.AssertActualEqualsExpected(m, opts.IfApiMachineryElseKyaml(
-		fmt.Sprintf(expFmt, `    prometheus.io/port: "8080"
-    prometheus.io/scrape: "true"
-    service.alpha.kubernetes.io/tolerate-unready-endpoints: "true"`),
-		fmt.Sprintf(expFmt, `    prometheus.io/port: 8080
-    prometheus.io/scrape: true
-    service.alpha.kubernetes.io/tolerate-unready-endpoints: true`)))
+`)
 }
 
 func TestFnContainerTransformer(t *testing.T) {
diff --git a/api/krusty/variableref_test.go b/api/krusty/variableref_test.go
index 41b55ffcf..e2c95591d 100644
--- a/api/krusty/variableref_test.go
+++ b/api/krusty/variableref_test.go
@@ -757,9 +757,9 @@ kind: Service
 metadata:
   annotations:
     prometheus.io/path: _status/vars
-    prometheus.io/port: %s
-    prometheus.io/scrape: %s
-    service.alpha.kubernetes.io/tolerate-unready-endpoints: %s
+    prometheus.io/port: "8080"
+    prometheus.io/scrape: "true"
+    service.alpha.kubernetes.io/tolerate-unready-endpoints: "true"
   labels:
     app: cockroachdb
   name: dev-base-cockroachdb
@@ -929,12 +929,8 @@ metadata:
 `
 	th.AssertActualEqualsExpected(m,
 		opts.IfApiMachineryElseKyaml(
-			fmt.Sprintf(
-				expFmt,
-				`"8080"`, `"true"`, `"true"`, `8080`, `8080`, `8080`, `8080`),
-			fmt.Sprintf(
-				expFmt,
-				`8080`, `true`, `true`, `"8080"`, `"8080"`, `"8080"`, `"8080"`),
+			fmt.Sprintf(expFmt, `8080`, `8080`, `8080`, `8080`),
+			fmt.Sprintf(expFmt, `"8080"`, `"8080"`, `"8080"`, `"8080"`),
 		))
 }
 
diff --git a/kyaml/yaml/datamap.go b/kyaml/yaml/datamap.go
index b3e7d5683..3181ff30f 100644
--- a/kyaml/yaml/datamap.go
+++ b/kyaml/yaml/datamap.go
@@ -52,11 +52,13 @@ func makeConfigMapValueRNode(s string) (field string, rN *RNode) {
 }
 
 func (rn *RNode) LoadMapIntoSecretData(m map[string]string) error {
+	mapNode, err := rn.Pipe(LookupCreate(MappingNode, DataField))
+	if err != nil {
+		return err
+	}
 	for _, k := range SortedMapKeys(m) {
 		vrN := makeSecretValueRNode(m[k])
-		if _, err := rn.Pipe(
-			LookupCreate(MappingNode, DataField),
-			SetField(k, vrN)); err != nil {
+		if _, err := mapNode.Pipe(SetField(k, vrN)); err != nil {
 			return err
 		}
 	}
diff --git a/kyaml/yaml/rnode.go b/kyaml/yaml/rnode.go
index a8131705c..f0e001cfe 100644
--- a/kyaml/yaml/rnode.go
+++ b/kyaml/yaml/rnode.go
@@ -372,18 +372,7 @@ func (rn *RNode) GetAnnotations() (map[string]string, error) {
 
 // SetAnnotations tries to set the metadata annotations field.
 func (rn *RNode) SetAnnotations(m map[string]string) error {
-	meta, err := rn.Pipe(Lookup(MetadataField))
-	if err != nil {
-		return err
-	}
-	if len(m) == 0 {
-		if meta == nil {
-			return nil
-		}
-		return meta.PipeE(Clear(AnnotationsField))
-	}
-	return rn.SetMapField(
-		NewMapRNode(&m), MetadataField, AnnotationsField)
+	return rn.setMapInMetadata(m, AnnotationsField)
 }
 
 // GetLabels gets the metadata labels field.
@@ -397,18 +386,32 @@ func (rn *RNode) GetLabels() (map[string]string, error) {
 
 // SetLabels sets the metadata labels field.
 func (rn *RNode) SetLabels(m map[string]string) error {
+	return rn.setMapInMetadata(m, LabelsField)
+}
+
+// This established proper quoting on string values, and sorts by key.
+func (rn *RNode) setMapInMetadata(m map[string]string, field string) error {
 	meta, err := rn.Pipe(Lookup(MetadataField))
 	if err != nil {
 		return err
 	}
-	if len(m) == 0 {
-		if meta == nil {
-			return nil
-		}
-		return meta.PipeE(Clear(LabelsField))
+	if err = meta.PipeE(Clear(field)); err != nil {
+		return err
 	}
-	return rn.SetMapField(
-		NewMapRNode(&m), MetadataField, LabelsField)
+	if len(m) == 0 {
+		return nil
+	}
+	mapNode, err := meta.Pipe(LookupCreate(MappingNode, field))
+	if err != nil {
+		return err
+	}
+	for _, k := range SortedMapKeys(m) {
+		if _, err := mapNode.Pipe(
+			SetField(k, NewStringRNode(m[k]))); err != nil {
+			return err
+		}
+	}
+	return nil
 }
 
 func (rn *RNode) SetMapField(value *RNode, path ...string) error {
diff --git a/plugin/builtin/annotationstransformer/AnnotationsTransformer_test.go b/plugin/builtin/annotationstransformer/AnnotationsTransformer_test.go
index 8c35f74a7..da11974bc 100644
--- a/plugin/builtin/annotationstransformer/AnnotationsTransformer_test.go
+++ b/plugin/builtin/annotationstransformer/AnnotationsTransformer_test.go
@@ -9,8 +9,12 @@ import (
 	kusttest_test "sigs.k8s.io/kustomize/api/testutils/kusttest"
 )
 
-var (
-	config = `
+func TestAnnotationsTransformer(t *testing.T) {
+	th := kusttest_test.MakeEnhancedHarness(t).
+		PrepBuiltin("AnnotationsTransformer")
+	defer th.Reset()
+
+	th.RunTransformerAndCheckResult(`
 apiVersion: builtin
 kind: AnnotationsTransformer
 metadata:
@@ -18,11 +22,14 @@ metadata:
 annotations:
   app: myApp
   greeting/morning: a string with blanks
+  booleanNaked: true
+  booleanQuoted: "true"
+  numberNaked: 42
+  numberQuoted: "42"
 fieldSpecs:
   - path: metadata/annotations
     create: true
-`
-	input = `
+`, `
 apiVersion: v1
 kind: Service
 metadata:
@@ -30,25 +37,20 @@ metadata:
 spec:
   ports:
   - port: 7002
-`
-	expectedOutput = `
+`, `
 apiVersion: v1
 kind: Service
 metadata:
   annotations:
     app: myApp
+    booleanNaked: "true"
+    booleanQuoted: "true"
     greeting/morning: a string with blanks
+    numberNaked: "42"
+    numberQuoted: "42"
   name: myService
 spec:
   ports:
   - port: 7002
-`
-)
-
-func TestAnnotationsTransformer(t *testing.T) {
-	th := kusttest_test.MakeEnhancedHarness(t).
-		PrepBuiltin("AnnotationsTransformer")
-	defer th.Reset()
-
-	th.RunTransformerAndCheckResult(config, input, expectedOutput)
+`)
 }