This paper presents a surgical treatment protocol known as EP-DDS (etiology identification, primary wound closure, debridement, decontamination, and stability of wound). The treatment protocol can be achieved in five steps. First, identify etiologic factors associated with peri-implantitis to determine whether or not the defects can be treated with this protocol. Second, in order to achieve primary wound coverage, ensure there is undisturbed wound healing, which may involve using procedures such as removing an existing prosthesis and performing tension-releasing flap design. Third, perform proper debridement of the inflamed granulomatous tissues to ensure the wound is free of any inflamed remnants. Fourth, conduct implant-surface decontamination by using a titanium brush or lasers. And finally, place appropriate space fillers (bone grafts and membrane) for wound stability. The three cases that have been successfully treated with the EP-DDS surgical protocol suggest it is a feasible surgical approach to obtain good infrabony defect bone fill (5.5-mm average) around the defects (buccal, mesial, lingual, and distal). Nonetheless, future randomized clinical trials with larger sample sizes and longer follow-ups are needed to further validate this treatment protocol.