diff --git a/api/internal/builtins/PatchTransformer.go b/api/internal/builtins/PatchTransformer.go
index 278d10093..442291d11 100644
--- a/api/internal/builtins/PatchTransformer.go
+++ b/api/internal/builtins/PatchTransformer.go
@@ -89,7 +89,10 @@ func (p *PatchTransformerPlugin) Transform(m resmap.ResMap) error {
 	if p.smPatches != nil {
 		return p.transformStrategicMerge(m)
 	}
-	return p.transformJson6902(m)
+	if p.jsonPatches != nil {
+		return p.transformJson6902(m)
+	}
+	return nil
 }
 
 // transformStrategicMerge applies each loaded strategic merge patch
diff --git a/plugin/builtin/patchtransformer/PatchTransformer.go b/plugin/builtin/patchtransformer/PatchTransformer.go
index 77e5439b0..4a2be54bf 100644
--- a/plugin/builtin/patchtransformer/PatchTransformer.go
+++ b/plugin/builtin/patchtransformer/PatchTransformer.go
@@ -94,7 +94,10 @@ func (p *plugin) Transform(m resmap.ResMap) error {
 	if p.smPatches != nil {
 		return p.transformStrategicMerge(m)
 	}
-	return p.transformJson6902(m)
+	if p.jsonPatches != nil {
+		return p.transformJson6902(m)
+	}
+	return nil
 }
 
 // transformStrategicMerge applies each loaded strategic merge patch