diff --git a/controllers/storagecluster/noobaa_system_reconciler.go b/controllers/storagecluster/noobaa_system_reconciler.go
index 1eaca63359..18c543df04 100644
--- a/controllers/storagecluster/noobaa_system_reconciler.go
+++ b/controllers/storagecluster/noobaa_system_reconciler.go
@@ -161,10 +161,15 @@ func (r *StorageClusterReconciler) setNooBaaDesiredState(nb *nbv1.NooBaa, sc *oc
 	placement := getPlacement(sc, component)
 
 	nb.Spec.Tolerations = placement.Tolerations
-	// if we are "noobaa-standalone" and placement is not set - don't set affinity
+
 	if !r.IsNoobaaStandalone || ok {
+		// Add affinity if not in noobaa-standalone mode or if placement is specified
 		nb.Spec.Affinity = &corev1.Affinity{NodeAffinity: placement.NodeAffinity}
+	} else if nb.Spec.Affinity != nil {
+		// Clear the affinity if it was set previously to handle upgrades
+		nb.Spec.Affinity = nil
 	}
+
 	nb.Spec.DBVolumeResources = &corev1.VolumeResourceRequirements{
 		Limits:   dBVolumeResources.Limits,
 		Requests: dBVolumeResources.Requests,