Background: The recently published Clinical Practice Guidelines (CPGs) for the treatment of stages I–IV periodontitis provided evidence‐based recommendations for treating periodontitis patients, defined according to the 2018 classification. Peri‐implant diseases were also re‐defined in the 2018 classification. It is well established that both peri‐implant mucositis and peri‐implantitis are highly prevalent. In addition, peri‐implantitis is particularly challenging to manage and is accompanied by significant morbidity.Aim: To develop an S3 level CPG for the prevention and treatment of peri‐implant diseases, focusing on the implementation of interdisciplinary approaches required to prevent the development of peri‐implant diseases or their recurrence, and to treat/rehabilitate patients with dental implants following the development of peri‐implant diseases.Materials and Methods: This S3 level CPG was developed by the European Federation of Periodontology, following methodological guidance from the Association of Scientific Medical Societies in Germany and the Grading of Recommendations Assessment, Development and Evaluation process. A rigorous and transparent process included synthesis of relevant research in 13 specifically commissioned systematic reviews, evaluation of the quality and strength of evidence, formulation of specific recommendations, and a structured consensus process involving leading experts and a broad base of stakeholders.Results: The S3 level CPG for the prevention and treatment of peri‐implant diseases culminated in the recommendation for implementation of various different interventions before, during and after implant placement/loading. Prevention of peri‐implant diseases should commence when dental implants are planned, surgically placed and prosthetically loaded. Once the implants are loaded and in function, a supportive peri‐implant care programme should be structured, including periodical assessment of peri‐implant tissue health. If peri‐implant mucositis or peri‐implantitis are detected, appropriate treatments for their management must be rendered.Conclusion: The present S3 level CPG informs clinical practice, health systems, policymakers and, indirectly, the public on the available and most effective modalities to maintain healthy peri‐implant tissues, and to manage peri‐implant diseases, according to the available evidence at the time of publication.