Objectives: To compare the efficacy of three mechanical procedures for surgically treating peri-implantitis. Materials and Methods: In a randomized, prospective, parallel-group study, 47 patients with peri-implantitis were treated with (a) plastic curettes (n = 15 patients, 25 implants), (b) an air-abrasive device (Perio-Flow®, n = 16 patients,22 implants), or (c) a titanium brush (Ti-Brush®, n = 16 patients, 23 implants). Patients were assessed for the following measures at three timepoints (baseline, and three and six months after surgery): plaque index, bleeding on probing, gingival index, probing pocket depth (PPD), relative attachment level, and bone loss. Treatment outcome was considered successful when the implant was still present with PPD ≤ 5 mm, no bleeding on probing, and no further mean bone loss ≥ 0.5 mm. Results: A greater reduction of gingival index and PPD was observed in the titanium brush group than in the other groups at six months (P < 0.001). Relative attachment level decreased from baseline in each group at three months but was more marked in the titanium brush group (P < 0.001). At six months, there was less bone loss in the titanium brush group than in the plastic curette group (P < 0.001; linear mixed model and Kruskal–Wallis). A successful outcome was observed in 22% of implants in the plastic curette group, 27% in the Perio-Flow® group, and 33% in the Ti-Brush® group. Conclusions: The titanium brush and glycine air-polishing device were more effective than the other methods, but treatment success remained low. Combining mechanical procedures with antimicrobials and/or antibiotics might be a more effective strategy and warrants careful investigation.