Purpose: The available scientific evidence on the effectiveness of the surgical treatment of peri-implantitis is limited. The aim of this study was to assess the risk of recurrence or disease progression in patients with peri-implantitis that underwent surgical treatment. Materials and Methods: A retrospective cohort study was carried out in patients subjected to peri-implant surgery between 2015 and 2021, and with a minimum follow-up of 12 months. Data were analyzed using simple binary logistic regression models at patient level and generalized estimation equations at implant level. Results: A total of 34 patients and 103 implants were analyzed (70 undergoing resective techniques and 33 regenerative procedures). Fifteen patients (44.12%) experienced peri-implantitis recurrence and one patient (2.9%) lost one implant. No differences were found between the surgical techniques (p = 0.56). A history of periodontitis (ORa = 4.62; 95%CI: 1.14 to 18.75; p = 0.032), maxillary location (ORa = 9.69; 95%CI: 1.81 to 51.87; p = 0.008) and two implants treated per procedure (ORa = 31.68; 95%CI: 3.91 to 256.54; p = 0.001) were seen to increase the risk of recurrence. Conclusions: Almost half of all patients (44%) undergoing surgical treatment of periimplantitis will present disease progression or recurrence. This risk seems to be higher in patients with several treated implants, with a history of periodontal disease, or when the maxilla is involved.