diff --git a/cmd/transform/transform.go b/cmd/transform/transform.go
index 95080bcd..99eef938 100644
--- a/cmd/transform/transform.go
+++ b/cmd/transform/transform.go
@@ -214,6 +214,7 @@ func (o *Options) run() error {
 	}
 
 	var instructionStages []string
+	var instructionPluginStages []string
 	var instructionStageOptionals map[string]map[string]string
 	if o.InstructionsFile != "" {
 		instructionsFilePath, err := filepath.Abs(o.InstructionsFile)
@@ -226,7 +227,8 @@ func (o *Options) run() error {
 			log.Errorf("Failed to load instructions file %q: %v", instructionsFilePath, err)
 			return err
 		}
-		instructionStages = internalTransform.GenerateStageDirNames(cfg.StageNames())
+		instructionPluginStages = cfg.StageNames()
+		instructionStages = internalTransform.GenerateStageDirNames(instructionPluginStages)
 		instructionStageOptionals, err = cfg.StageOptionals()
 		if err != nil {
 			return fmt.Errorf("invalid instructions file %q: %w", instructionsFilePath, err)
@@ -290,7 +292,7 @@ func (o *Options) run() error {
 			log.Errorf("Failed to reconcile instruction stages: %v", err)
 			return err
 		}
-		for _, stageName := range instructionStages {
+		for i, stageName := range instructionStages {
 			stageDir := filepath.Join(transformDir, stageName)
 			_, err := os.Stat(stageDir)
 			stageExists := err == nil
@@ -310,7 +312,9 @@ func (o *Options) run() error {
 				Stages: []string{stageName},
 			}
 			log.Infof("Running stage: %s", stageName)
-			if err := o.runStageWithCleanup(orchestrator, selector, stageDir, !stageExists, log); err != nil {
+			stageOrchestrator := *orchestrator
+			stageOrchestrator.StageOptionalFlags = stageOptionalsForPlugin(instructionStageOptionals, instructionPluginStages[i])
+			if err := o.runStageWithCleanup(&stageOrchestrator, selector, stageDir, !stageExists, log); err != nil {
 				log.Errorf("Failed to run stage %q: %v", stageName, err)
 				return err
 			}
@@ -388,6 +392,16 @@ func (o *Options) run() error {
 	return nil
 }
 
+// stageOptionalsForPlugin restricts instruction optionals to the plugin being
+// run because instructions stages are executed individually.
+func stageOptionalsForPlugin(optionals map[string]map[string]string, pluginName string) map[string]map[string]string {
+	flags, ok := optionals[pluginName]
+	if !ok {
+		return nil
+	}
+	return map[string]map[string]string{pluginName: flags}
+}
+
 // parseStageOptionals parses --stage-optionals values from "StageName=JSON" format
 // into a map of stage name to optional flags.
 func parseStageOptionals(values []string) (map[string]map[string]string, error) {
diff --git a/cmd/transform/transform_test.go b/cmd/transform/transform_test.go
index 9e5bef98..e6614239 100644
--- a/cmd/transform/transform_test.go
+++ b/cmd/transform/transform_test.go
@@ -1253,6 +1253,63 @@ func TestRun_InstructionsFileAndStageOptionalsConflict(t *testing.T) {
 	}
 }
 
+func TestStageOptionalsForPlugin(t *testing.T) {
+	optionals := map[string]map[string]string{
+		"KubernetesPlugin": {"strip-default-rbac": "true"},
+		"OpenShiftPlugin":  {"strip-default-cabundle": "true"},
+	}
+
+	tests := []struct {
+		name     string
+		plugin   string
+		expected map[string]map[string]string
+	}{
+		{
+			name:   "returns only KubernetesPlugin optionals",
+			plugin: "KubernetesPlugin",
+			expected: map[string]map[string]string{
+				"KubernetesPlugin": {"strip-default-rbac": "true"},
+			},
+		},
+		{
+			name:   "returns only OpenShiftPlugin optionals",
+			plugin: "OpenShiftPlugin",
+			expected: map[string]map[string]string{
+				"OpenShiftPlugin": {"strip-default-cabundle": "true"},
+			},
+		},
+		{
+			name:     "returns nil for stage without optionals",
+			plugin:   "CustomEdits",
+			expected: nil,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			got := stageOptionalsForPlugin(optionals, tt.plugin)
+			if len(got) != len(tt.expected) {
+				t.Fatalf("expected %d stage optionals, got %d: %v", len(tt.expected), len(got), got)
+			}
+			for stage, expectedFlags := range tt.expected {
+				gotFlags, ok := got[stage]
+				if !ok {
+					t.Errorf("missing optionals for stage %q", stage)
+					continue
+				}
+				if len(gotFlags) != len(expectedFlags) {
+					t.Errorf("stage %q: expected %d flags, got %d", stage, len(expectedFlags), len(gotFlags))
+				}
+				for key, expectedValue := range expectedFlags {
+					if gotFlags[key] != expectedValue {
+						t.Errorf("stage %q flag %q: expected %q, got %q", stage, key, expectedValue, gotFlags[key])
+					}
+				}
+			}
+		})
+	}
+}
+
 func TestValidate_MissingExportDir_FailsBeforeRun(t *testing.T) {
 	tmpDir := t.TempDir()
 	transformDir := filepath.Join(tmpDir, "transform")