Peri-implant diseases are defined as bacterial plaque-induced inflammatory conditions affecting implant-surrounding tissues and are classified as peri-implant mucositis and peri-implantitis. Peri-implant mucositis is characterized by an inflammatory lesion that resides in the soft tissue compartment, whereas at peri-implantitis sites the lesions also feature progressive loss of implant-supporting bone. Inflammation resolution and disease progression arrestment are the main therapeutic endpoints of the treatment of peri-implant diseases. The present position paper displays the current evidence and clinical recommendations of the European Association for Osseointegration for the treatment of peri-implant diseases. Mechanical biofilm removal along with the reinforcement of patient-administered oral hygiene is considered the standard treatment for managing peri-implant mucositis. It is recommended to assess the outcomes of peri-implant mucositis treatment 2 to 3 months after therapy, and repeated intervention should be considered in the absence of treatment success. Peri-implantitis treatment should follow a stepwise treatment approach, starting with nonsurgical treatment followed by surgical intervention, if that is not sufficient. Surgical peri-implantitis therapies include nonreconstructive, reconstructive, and combined treatment modalities. Implantoplasty may be advocated for the treatment of supracrestal peri-implant defects, whereas reconstructive therapy is indicated at peri-implantitis sites featuring intraosseous defects with a depth ≥ 3 mm. Adjunctive reconstructive measures may be beneficial in enhancing radiographic defect fill and maintaining postoperative soft tissue levels, which may have a great impact in esthetic cases. The adjunctive use of systemic antibiotics during surgical therapy does not seem to improve the clinical outcomes. Regular supportive peri-implant therapy with biofilm removal should be an integral part of the treatment protocol for peri-implant diseases. In the presence of advanced bone loss around implants that do not play a strategic role in masticatory function, implant removal may be considered immediately.