diff --git a/pkg/builder/controller.go b/pkg/builder/controller.go
index 0fee47b8af..b3324eb54e 100644
--- a/pkg/builder/controller.go
+++ b/pkg/builder/controller.go
@@ -245,7 +245,9 @@ func (blder *Builder) doController(r reconcile.Reconciler) error {
 		return err
 	}
 	ctrlOptions := blder.ctrlOptions
-	ctrlOptions.Reconciler = r
+	if ctrlOptions.Reconciler == nil {
+		ctrlOptions.Reconciler = r
+	}
 	blder.ctrl, err = newController(name, blder.mgr, ctrlOptions)
 	return err
 }
diff --git a/pkg/builder/controller_test.go b/pkg/builder/controller_test.go
index b2913d63e0..3693bbaee6 100644
--- a/pkg/builder/controller_test.go
+++ b/pkg/builder/controller_test.go
@@ -41,6 +41,12 @@ import (
 	"sigs.k8s.io/controller-runtime/pkg/source"
 )
 
+type typedNoop struct{}
+
+func (typedNoop) Reconcile(reconcile.Request) (reconcile.Result, error) {
+	return reconcile.Result{}, nil
+}
+
 var _ = Describe("application", func() {
 	var stop chan struct{}
 
@@ -151,6 +157,27 @@ var _ = Describe("application", func() {
 			Expect(instance).NotTo(BeNil())
 		})
 
+		It("should prefer reconciler from options during creation of controller", func() {
+			newController = func(name string, mgr manager.Manager, options controller.Options) (controller.Controller, error) {
+				if options.Reconciler != (typedNoop{}) {
+					return nil, fmt.Errorf("Custom reconciler expected %T but found %T", typedNoop{}, options.Reconciler)
+				}
+				return controller.New(name, mgr, options)
+			}
+
+			By("creating a controller manager")
+			m, err := manager.New(cfg, manager.Options{})
+			Expect(err).NotTo(HaveOccurred())
+
+			instance, err := ControllerManagedBy(m).
+				For(&appsv1.ReplicaSet{}).
+				Owns(&appsv1.ReplicaSet{}).
+				WithOptions(controller.Options{Reconciler: typedNoop{}}).
+				Build(noop)
+			Expect(err).NotTo(HaveOccurred())
+			Expect(instance).NotTo(BeNil())
+		})
+
 		It("should allow multiple controllers for the same kind", func() {
 			By("creating a controller manager")
 			m, err := manager.New(cfg, manager.Options{})