diff --git a/api/builtins/PatchJson6902Transformer.go b/api/builtins/PatchJson6902Transformer.go
index dfe4db43b..cb02c4241 100644
--- a/api/builtins/PatchJson6902Transformer.go
+++ b/api/builtins/PatchJson6902Transformer.go
@@ -12,6 +12,7 @@ import (
 	"sigs.k8s.io/kustomize/api/ifc"
 	"sigs.k8s.io/kustomize/api/resmap"
 	"sigs.k8s.io/kustomize/api/types"
+	"sigs.k8s.io/kustomize/kyaml/kio/kioutil"
 	"sigs.k8s.io/yaml"
 )
 
@@ -78,12 +79,23 @@ func (p *PatchJson6902TransformerPlugin) Transform(m resmap.ResMap) error {
 		return err
 	}
 	for _, res := range resources {
+		internalAnnotations := kioutil.GetInternalAnnotations(&res.RNode)
+
 		err = res.ApplyFilter(patchjson6902.Filter{
 			Patch: p.JsonOp,
 		})
 		if err != nil {
 			return err
 		}
+
+		annotations := res.GetAnnotations()
+		for key, value := range internalAnnotations {
+			annotations[key] = value
+		}
+		err = res.SetAnnotations(annotations)
+		if err != nil {
+			return err
+		}
 	}
 	return nil
 }
diff --git a/api/builtins/PatchTransformer.go b/api/builtins/PatchTransformer.go
index 07038af1e..dc51748c8 100644
--- a/api/builtins/PatchTransformer.go
+++ b/api/builtins/PatchTransformer.go
@@ -12,6 +12,7 @@ import (
 	"sigs.k8s.io/kustomize/api/resmap"
 	"sigs.k8s.io/kustomize/api/resource"
 	"sigs.k8s.io/kustomize/api/types"
+	"sigs.k8s.io/kustomize/kyaml/kio/kioutil"
 	"sigs.k8s.io/yaml"
 )
 
@@ -111,12 +112,19 @@ func (p *PatchTransformerPlugin) transformJson6902(m resmap.ResMap, patch jsonpa
 	}
 	for _, res := range resources {
 		res.StorePreviousId()
+		internalAnnotations := kioutil.GetInternalAnnotations(&res.RNode)
 		err = res.ApplyFilter(patchjson6902.Filter{
 			Patch: p.Patch,
 		})
 		if err != nil {
 			return err
 		}
+
+		annotations := res.GetAnnotations()
+		for key, value := range internalAnnotations {
+			annotations[key] = value
+		}
+		err = res.SetAnnotations(annotations)
 	}
 	return nil
 }
diff --git a/api/krusty/multiplepatch_test.go b/api/krusty/multiplepatch_test.go
index 5fb5fed3f..9935fba53 100644
--- a/api/krusty/multiplepatch_test.go
+++ b/api/krusty/multiplepatch_test.go
@@ -1646,3 +1646,64 @@ spec:
   type: NodePort
 `)
 }
+
+// test for #4111
+func TestPatchPreservesInternalAnnotations(t *testing.T) {
+	th := kusttest_test.MakeHarness(t)
+	th.WriteK(".", `
+nameSuffix: -abc
+resources:
+  - fluentd.yaml
+patchesJson6902:
+  - path: patch.yaml
+    target:
+      name: fluentd-sa
+      kind: ServiceAccount
+      version: v1
+`)
+	th.WriteF("fluentd.yaml", `
+apiVersion: v1
+kind: DaemonSet
+metadata:
+  name: fluentd
+spec:
+  template:
+    spec:
+      containers:
+        - image: fluentd:latest 
+          name: fluentd
+      serviceAccountName: fluentd-sa
+---
+apiVersion: v1
+kind: ServiceAccount
+metadata:
+  name: fluentd-sa
+`)
+	th.WriteF("patch.yaml", `
+- op: add
+  path: /metadata/annotations
+  value:
+    note: this is a test annotation
+`)
+	m := th.Run(".", th.MakeDefaultOptions())
+	th.AssertActualEqualsExpected(m, `
+apiVersion: v1
+kind: DaemonSet
+metadata:
+  name: fluentd-abc
+spec:
+  template:
+    spec:
+      containers:
+      - image: fluentd:latest
+        name: fluentd
+      serviceAccountName: fluentd-sa-abc
+---
+apiVersion: v1
+kind: ServiceAccount
+metadata:
+  annotations:
+    note: this is a test annotation
+  name: fluentd-sa-abc
+`)
+}
diff --git a/plugin/builtin/patchjson6902transformer/PatchJson6902Transformer.go b/plugin/builtin/patchjson6902transformer/PatchJson6902Transformer.go
index 3e4f619c9..19f1c78d2 100644
--- a/plugin/builtin/patchjson6902transformer/PatchJson6902Transformer.go
+++ b/plugin/builtin/patchjson6902transformer/PatchJson6902Transformer.go
@@ -13,6 +13,7 @@ import (
 	"sigs.k8s.io/kustomize/api/ifc"
 	"sigs.k8s.io/kustomize/api/resmap"
 	"sigs.k8s.io/kustomize/api/types"
+	"sigs.k8s.io/kustomize/kyaml/kio/kioutil"
 	"sigs.k8s.io/yaml"
 )
 
@@ -82,12 +83,23 @@ func (p *plugin) Transform(m resmap.ResMap) error {
 		return err
 	}
 	for _, res := range resources {
+		internalAnnotations := kioutil.GetInternalAnnotations(&res.RNode)
+
 		err = res.ApplyFilter(patchjson6902.Filter{
 			Patch: p.JsonOp,
 		})
 		if err != nil {
 			return err
 		}
+
+		annotations := res.GetAnnotations()
+		for key, value := range internalAnnotations {
+			annotations[key] = value
+		}
+		err = res.SetAnnotations(annotations)
+		if err != nil {
+			return err
+		}
 	}
 	return nil
 }
diff --git a/plugin/builtin/patchjson6902transformer/go.mod b/plugin/builtin/patchjson6902transformer/go.mod
index 8d096afd8..9ca52c2d9 100644
--- a/plugin/builtin/patchjson6902transformer/go.mod
+++ b/plugin/builtin/patchjson6902transformer/go.mod
@@ -6,6 +6,7 @@ require (
 	github.com/evanphx/json-patch v4.11.0+incompatible
 	github.com/pkg/errors v0.9.1
 	sigs.k8s.io/kustomize/api v0.8.9
+	sigs.k8s.io/kustomize/kyaml v0.12.0
 	sigs.k8s.io/yaml v1.2.0
 )
 
diff --git a/plugin/builtin/patchtransformer/PatchTransformer.go b/plugin/builtin/patchtransformer/PatchTransformer.go
index 54fe9dedb..2d02cf28f 100644
--- a/plugin/builtin/patchtransformer/PatchTransformer.go
+++ b/plugin/builtin/patchtransformer/PatchTransformer.go
@@ -13,6 +13,7 @@ import (
 	"sigs.k8s.io/kustomize/api/resmap"
 	"sigs.k8s.io/kustomize/api/resource"
 	"sigs.k8s.io/kustomize/api/types"
+	"sigs.k8s.io/kustomize/kyaml/kio/kioutil"
 	"sigs.k8s.io/yaml"
 )
 
@@ -115,12 +116,19 @@ func (p *plugin) transformJson6902(m resmap.ResMap, patch jsonpatch.Patch) error
 	}
 	for _, res := range resources {
 		res.StorePreviousId()
+		internalAnnotations := kioutil.GetInternalAnnotations(&res.RNode)
 		err = res.ApplyFilter(patchjson6902.Filter{
 			Patch: p.Patch,
 		})
 		if err != nil {
 			return err
 		}
+
+		annotations := res.GetAnnotations()
+		for key, value := range internalAnnotations {
+			annotations[key] = value
+		}
+		err = res.SetAnnotations(annotations)
 	}
 	return nil
 }
diff --git a/plugin/builtin/patchtransformer/go.mod b/plugin/builtin/patchtransformer/go.mod
index 59744066f..3a9b85e01 100644
--- a/plugin/builtin/patchtransformer/go.mod
+++ b/plugin/builtin/patchtransformer/go.mod
@@ -5,6 +5,7 @@ go 1.16
 require (
 	github.com/evanphx/json-patch v4.11.0+incompatible
 	sigs.k8s.io/kustomize/api v0.8.9
+	sigs.k8s.io/kustomize/kyaml v0.12.0
 	sigs.k8s.io/yaml v1.2.0
 )