diff --git a/pkg/target/kusttarget.go b/pkg/target/kusttarget.go
index 035bed892..63cdac8ee 100644
--- a/pkg/target/kusttarget.go
+++ b/pkg/target/kusttarget.go
@@ -32,7 +32,6 @@ import (
 	"sigs.k8s.io/kustomize/pkg/fs"
 	interror "sigs.k8s.io/kustomize/pkg/internal/error"
 	"sigs.k8s.io/kustomize/pkg/loader"
-	"sigs.k8s.io/kustomize/pkg/patch"
 	patchtransformer "sigs.k8s.io/kustomize/pkg/patch/transformer"
 	"sigs.k8s.io/kustomize/pkg/resmap"
 	"sigs.k8s.io/kustomize/pkg/resource"
@@ -60,13 +59,14 @@ func NewKustTarget(
 		return nil, err
 	}
 
-	var m types.Kustomization
-	err = unmarshal(content, &m)
+	var k types.Kustomization
+	err = unmarshal(content, &k)
 	if err != nil {
 		return nil, err
 	}
+	k.DealWithDeprecatedFields()
 	return &KustTarget{
-		kustomization: &m,
+		kustomization: &k,
 		ldr:           ldr,
 		fSys:          fSys,
 		tcfg:          tcfg,
@@ -157,9 +157,6 @@ func (kt *KustTarget) loadCustomizedResMap() (resmap.ResMap, error) {
 		return nil, err
 	}
 
-	kt.kustomization.PatchesStrategicMerge = patch.Append(
-		kt.kustomization.PatchesStrategicMerge,
-		kt.kustomization.Patches...)
 	patches, err := resource.NewResourceSliceFromPatches(
 		kt.ldr, kt.kustomization.PatchesStrategicMerge, kt.decoder)
 	if err != nil {
diff --git a/pkg/types/kustomization.go b/pkg/types/kustomization.go
index 3e00325dc..1aa35540e 100644
--- a/pkg/types/kustomization.go
+++ b/pkg/types/kustomization.go
@@ -91,6 +91,18 @@ type Kustomization struct {
 	ImageTags []ImageTag `json:"imageTags,omitempty" yaml:"imageTags,omitempty"`
 }
 
+// DealWithDeprecatedFields should be called immediately after
+// loading from storage.
+func (k *Kustomization) DealWithDeprecatedFields() {
+	// The Patches field, meant to hold StrategicMerge patches,
+	// is deprecated. Append anything found there to the
+	// PatchesStrategicMerge field.
+	// This happened when the PatchesJson6902 field was introduced.
+	k.PatchesStrategicMerge = patch.Append(
+		k.PatchesStrategicMerge, k.Patches...)
+	k.Patches = []string{}
+}
+
 // ConfigMapArgs contains the metadata of how to generate a configmap.
 type ConfigMapArgs struct {
 	// Name of the configmap.