diff --git a/controllers/kustomization_generator.go b/controllers/kustomization_generator.go
index bf81600d7..307bb7da1 100644
--- a/controllers/kustomization_generator.go
+++ b/controllers/kustomization_generator.go
@@ -18,6 +18,7 @@ package controllers
 
 import (
 	"crypto/sha1"
+	"encoding/json"
 	"fmt"
 	"io/ioutil"
 	"os"
@@ -32,6 +33,8 @@ import (
 	kustypes "sigs.k8s.io/kustomize/api/types"
 	"sigs.k8s.io/yaml"
 
+	"github.com/fluxcd/pkg/apis/kustomize"
+
 	kustomizev1 "github.com/fluxcd/kustomize-controller/api/v1beta1"
 )
 
@@ -96,6 +99,21 @@ func (kg *KustomizeGenerator) WriteFile(dirPath string) (string, error) {
 		kus.Namespace = kg.kustomization.Spec.TargetNamespace
 	}
 
+	for _, m := range kg.kustomization.Spec.PatchesStrategicMerge {
+		kus.PatchesStrategicMerge = append(kus.PatchesStrategicMerge, kustypes.PatchStrategicMerge(m.String()))
+	}
+
+	for _, m := range kg.kustomization.Spec.PatchesJSON6902 {
+		patch, err := json.Marshal(m.Patch)
+		if err != nil {
+			return "", err
+		}
+		kus.PatchesJson6902 = append(kus.PatchesJson6902, kustypes.Patch{
+			Patch:  string(patch),
+			Target: adaptSelector(&m.Target),
+		})
+	}
+
 	for _, image := range kg.kustomization.Spec.Images {
 		newImage := kustypes.Image{
 			Name:    image.Name,
@@ -279,6 +297,20 @@ func (kg *KustomizeGenerator) generateLabelTransformer(checksum, dirPath string)
 	return nil
 }
 
+func adaptSelector(selector *kustomize.Selector) (output *kustypes.Selector) {
+	if selector != nil {
+		output = &kustypes.Selector{}
+		output.Gvk.Group = selector.Group
+		output.Gvk.Kind = selector.Kind
+		output.Gvk.Version = selector.Version
+		output.Name = selector.Name
+		output.Namespace = selector.Namespace
+		output.LabelSelector = selector.LabelSelector
+		output.AnnotationSelector = selector.AnnotationSelector
+	}
+	return
+}
+
 // buildKustomization wraps krusty.MakeKustomizer with the following settings:
 // - disable kyaml due to critical bugs like:
 //	 - https://github.com/kubernetes-sigs/kustomize/issues/3446
diff --git a/go.mod b/go.mod
index 365539dcf..67b8722c4 100644
--- a/go.mod
+++ b/go.mod
@@ -7,6 +7,7 @@ replace github.com/fluxcd/kustomize-controller/api => ./api
 require (
 	github.com/cyphar/filepath-securejoin v0.2.2
 	github.com/fluxcd/kustomize-controller/api v0.7.4
+	github.com/fluxcd/pkg/apis/kustomize v0.0.1
 	github.com/fluxcd/pkg/apis/meta v0.7.0
 	github.com/fluxcd/pkg/runtime v0.8.0
 	github.com/fluxcd/pkg/testserver v0.0.2