diff --git a/api/internal/plugins/utils/utils.go b/api/internal/plugins/utils/utils.go
index ffd10087a..821b3c859 100644
--- a/api/internal/plugins/utils/utils.go
+++ b/api/internal/plugins/utils/utils.go
@@ -4,6 +4,7 @@
 package utils
 
 import (
+	"encoding/json"
 	"fmt"
 	"os"
 	"path/filepath"
@@ -13,7 +14,6 @@ import (
 
 	"sigs.k8s.io/kustomize/api/filesys"
 	"sigs.k8s.io/kustomize/api/konfig"
-	"sigs.k8s.io/kustomize/api/resid"
 	"sigs.k8s.io/kustomize/api/resmap"
 	"sigs.k8s.io/kustomize/api/resource"
 	"sigs.k8s.io/kustomize/api/types"
@@ -148,50 +148,52 @@ func GetResMapWithIDAnnotation(rm resmap.ResMap) (resmap.ResMap, error) {
 // UpdateResMapValues updates the Resource value in the given ResMap
 // with the emitted Resource values in output.
 func UpdateResMapValues(pluginName string, h *resmap.PluginHelpers, output []byte, rm resmap.ResMap) error {
-	resFactory := h.ResmapFactory().RF()
+	mapFactory := h.ResmapFactory()
+	resFactory := mapFactory.RF()
 	resources, err := resFactory.SliceFromBytes(output)
 	if err != nil {
 		return err
 	}
+	// Don't use resources here, or error message will be unfriendly to plugin builders
+	newMap, err := mapFactory.NewResMapFromBytes([]byte{})
+	if err != nil {
+		return err
+	}
+
 	for _, r := range resources {
-		// for each emitted Resource, find the matching Resource in the original ResMap
-		// using its id
-		annotations := r.GetAnnotations()
-		idString, ok := annotations[idAnnotation]
-		// Transformer-generated resource--add to resMap
-		if !ok {
-			if err := rm.Append(r); err != nil {
-				return err
+		removeIDAnnotation(r) // stale--not manipulated by plugin transformers
+
+		// Add to the new map, checking for duplicates
+		if err := newMap.Append(r); err != nil {
+			prettyID, err := json.Marshal(r.CurId())
+			if err != nil {
+				prettyID = []byte(r.CurId().String())
 			}
-			continue
+			return fmt.Errorf("plugin %s generated duplicate resource: %s", pluginName, prettyID)
 		}
 
-		id := resid.ResId{}
-		err = yaml.Unmarshal([]byte(idString), &id)
+		// Add to or update the old map
+		oldIdx, err := rm.GetIndexOfCurrentId(r.CurId())
 		if err != nil {
 			return err
 		}
-
-		// Outdated ID is likely a duplicated resource--add to resMap
-		if !id.Equals(r.CurId()) {
-			removeIDAnnotation(r)
+		if oldIdx != -1 {
+			rm.GetByIndex(oldIdx).ResetPrimaryData(r)
+		} else {
 			if err := rm.Append(r); err != nil {
 				return err
 			}
-			continue
 		}
-
-		// Existing resource--update in resMap
-
-		res, err := rm.GetByCurrentId(id)
-		if err != nil {
-			return fmt.Errorf("unable to find unique match to %s", id.String())
-		}
-		removeIDAnnotation(r)
-
-		// update the resource value with the transformed object
-		res.ResetPrimaryData(r)
 	}
+
+	// Remove items the transformer deleted from the old map
+	for _, id := range rm.AllIds() {
+		newIdx, _ := newMap.GetIndexOfCurrentId(id)
+		if newIdx == -1 {
+			rm.Remove(id)
+		}
+	}
+
 	return nil
 }
 
diff --git a/plugin/someteam.example.com/v1/starlarkmixer/StarlarkMixer_test.go b/plugin/someteam.example.com/v1/starlarkmixer/StarlarkMixer_test.go
index 467179491..aa07ed1f6 100644
--- a/plugin/someteam.example.com/v1/starlarkmixer/StarlarkMixer_test.go
+++ b/plugin/someteam.example.com/v1/starlarkmixer/StarlarkMixer_test.go
@@ -4,6 +4,7 @@
 package starlarkmixer_test
 
 import (
+	"strings"
 	"testing"
 
 	kusttest_test "sigs.k8s.io/kustomize/api/testutils/kusttest"
@@ -29,6 +30,11 @@ metadata:
   name: some-cm
 data:
   foo: bar
+---
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: delete-me
 `)
 
 	th.AssertActualEqualsExpected(rm, `
@@ -59,3 +65,46 @@ metadata:
   name: net-new
 `)
 }
+
+func TestStarlarkMixerPlugin_duplicate_rejection(t *testing.T) {
+	th := kusttest_test.MakeEnhancedHarness(t)
+	defer th.Reset()
+
+	th.RunTransformerAndCheckError(`
+apiVersion: someteam.example.com/v1
+kind: StarlarkMixer
+metadata:
+  name: mixer-instance
+  annotations:
+    config.kubernetes.io/function: |
+      starlark:
+        path: mixer.star
+`,
+		`apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: some-cm
+data:
+  foo: bar
+---
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: some-cm-copy
+data:
+  foo: bar
+`,
+		func(t *testing.T, err error) {
+			if err == nil {
+				t.Fatal("expected error")
+			}
+			expectedErr := "plugin api: someteam.example.com/v1, " +
+				"kind: StarlarkMixer, " +
+				"name: mixer-instance generated duplicate " +
+				"resource: {\"version\":\"v1\",\"kind\":\"ConfigMap\",\"name\":\"some-cm-copy\"}"
+			if !strings.Contains(err.Error(), expectedErr) {
+				t.Fatalf("unexpected error: %s", err.Error())
+			}
+		},
+	)
+}