Surface decontamination in the reconstructive therapy of peri-implantitis is of paramount importance to achieve favorable outcomes. The objective of this single-center study, derived from a large multicenter clinical trial, was to analyze the electrolytic method (EM) as an adjunct to mechanical decontamination and compare it to hydrogen peroxide (HP), also used as an adjunct to mechanical decontamination, in the reconstructive therapy of peri-implantitis. At the 12-month follow-up (T2), 19 patients (n = 23 implants) completed the study. None of the tested modalities demonstrated superiority in the assessed clinical parameters. Only mucosal recession showed higher stability in the EM group. Similarly, radiographic marginal bone level gain and defect angle changes at T2 did not differ between the evaluated strategies. Notably, disease resolution was ~16% higher for the EM group; however, differences were not statistically significant. Additionally, it was demonstrated that pocket depth and the intrabony component depth at baseline were predictors of disease resolution. EM combined with mechanical instrumentation results in a safe and effective surface decontamination modality in the reconstructive therapy of peri-implantitis. This strategy resulted in a disease resolution rate of ~91%.