Deep bites can be treated by the intrusion of anterior teeth and the extrusion of the posterior teeth, or both, according to the exposure of the incisors in the smile. The aim of this paper is to propose a protocol to improve the effectiveness of deep bite treatments. Orthodontic movements are programmed following the “frog staging” protocol for the anterior teeth, the application of retention attachments and the overengineered final setup. Two case reports described the clinical and radiographic changes with orthodontic treatment using Invisalign clear aligners by applying this protocol.