Peri-implantitis is a common complication among patients receiving implant-supported restorative therapy, and it often requires surgical intervention for effective treatment. Understanding the specific configuration of the peri-implant bony defect and adjacent bone peaks is crucial for tailoring treatment strategies and improving outcomes. A decision tree for reconstructive peri-implantitis therapy has been developed based on the new classification of defect configurations (Classes I to V), guiding clinicians in selecting treatment options, including biomaterials, techniques, and healing approaches. Furthermore, clinicians are encouraged to consider various factors such as local predisposing factors (including soft tissue characteristics, prosthetic design, and implant position in a 3D perspective), clinical factors (surgeon skill and experience), and patient-related factors (such as local and systemic health, preferences, and cost) when evaluating reconstructive therapy options.