Treatment protocols for peri-implantitis include various decontamination procedures of the exposed implant surface, and their application is dependent on the stage of implant therapy, involving both non-surgical and surgical interventions, as appropriate. These implant surface decontamination procedures may be delivered using different approaches, such as mechanical/physical, chemical, photo/mechanical, adjuncts, or combinations thereof. In Part 1 of this two-part series, we reviewed the available evidence for the non-surgical and surgical management of peri-implantitis. In Part 2, we discuss different approaches for implant surface decontamination. CPD/Clinical Relevance: The pre-operative risk identification and management at both patient and site level, early diagnosis and regular supportive peri-implant care are fundamental for long term implant success and survival.