diff --git a/kyaml/kio/byteio_reader.go b/kyaml/kio/byteio_reader.go
index 4f20a52f5..7d0aeda79 100644
--- a/kyaml/kio/byteio_reader.go
+++ b/kyaml/kio/byteio_reader.go
@@ -43,6 +43,7 @@ type ByteReadWriter struct {
 
 	Results *yaml.RNode
 
+	NoWrap             bool
 	WrappingAPIVersion string
 	WrappingKind       string
 }
@@ -53,10 +54,15 @@ func (rw *ByteReadWriter) Read() ([]*yaml.RNode, error) {
 		OmitReaderAnnotations: rw.OmitReaderAnnotations,
 	}
 	val, err := b.Read()
-	rw.FunctionConfig = b.FunctionConfig
+	if rw.FunctionConfig == nil {
+		rw.FunctionConfig = b.FunctionConfig
+	}
 	rw.Results = b.Results
-	rw.WrappingAPIVersion = b.WrappingAPIVersion
-	rw.WrappingKind = b.WrappingKind
+
+	if !rw.NoWrap {
+		rw.WrappingAPIVersion = b.WrappingAPIVersion
+		rw.WrappingKind = b.WrappingKind
+	}
 	return val, errors.Wrap(err)
 }
 
diff --git a/kyaml/kio/byteio_readwriter_test.go b/kyaml/kio/byteio_readwriter_test.go
index e7cea1b2b..0e965186a 100644
--- a/kyaml/kio/byteio_readwriter_test.go
+++ b/kyaml/kio/byteio_readwriter_test.go
@@ -10,6 +10,7 @@ import (
 
 	"github.com/stretchr/testify/assert"
 	"sigs.k8s.io/kustomize/kyaml/kio"
+	"sigs.k8s.io/kustomize/kyaml/yaml"
 )
 
 func TestByteReadWriter(t *testing.T) {
@@ -226,6 +227,68 @@ metadata:
 `,
 			instance: kio.ByteReadWriter{KeepReaderAnnotations: true},
 		},
+
+		{
+			name: "manual_override_wrap",
+			input: `
+apiVersion: config.kubernetes.io/v1alpha1
+kind: ResourceList
+items:
+- kind: Deployment
+  spec:
+    replicas: 1
+- kind: Service
+  spec:
+    selectors:
+      foo: bar
+functionConfig:
+  a: b # something
+`,
+			expectedOutput: `
+kind: Deployment
+spec:
+  replicas: 1
+---
+kind: Service
+spec:
+  selectors:
+    foo: bar
+`,
+			instance: kio.ByteReadWriter{NoWrap: true},
+		},
+
+		{
+			name: "manual_override_function_config",
+			input: `
+apiVersion: config.kubernetes.io/v1alpha1
+kind: ResourceList
+items:
+- kind: Deployment
+  spec:
+    replicas: 1
+- kind: Service
+  spec:
+    selectors:
+      foo: bar
+functionConfig:
+  a: b # something
+`,
+			expectedOutput: `
+apiVersion: config.kubernetes.io/v1alpha1
+kind: ResourceList
+items:
+- kind: Deployment
+  spec:
+    replicas: 1
+- kind: Service
+  spec:
+    selectors:
+      foo: bar
+functionConfig:
+  c: d
+`,
+			instance: kio.ByteReadWriter{FunctionConfig: yaml.MustParse(`c: d`)},
+		},
 	}
 
 	for i := range testCases {