Background and aims: Peri-implantitis is a complex pathology, both in its diagnosis and in the identification of etiological causes. Although we have been studying more and more over the years to try to answer the many questions that remain regarding everything that circulates around this disease which affects implants, nothing has yet been taken as an official consensus regarding its surgical treatment. There are still many proposed protocols, each of which has been shown to have comforting results and promising prospects, but no total predictability. The aim of this case series is to assess the clinical outcomes of a mixed protocol for the regeneration of deep osseous defects. Materials and methods: The data and clinical records of 23 patients, with 29 implants affected by peri-implantitis treated surgically in private practice, were analyzed retrospectively. The method used for the surgical treatment was a mixed protocol of mechanical–chemical decontamination and bone regeneration with bovine xenograft. Results: All patients were followed for at least 2 years, averaging 28.9 months (a range of 24–38 months) with a reduction in the probing depth (PD) at one year from the initial 8.14 ± 1.156 mm to 3.72 ± 0.649 mm, and to 4.14 ± 1.093 mm at the final assessment. The differences between assessment time points were always statistically significant. The data regarding bleeding on probing (BoP) and suppuration also showed a statistically significant reduction at the final time point compared to the baseline. Only one patient, at 24 months, still showed BoP, suppuration, and a PD deeper than 5 mm, indicating a recurrence of the disease compared to the initial improvement of the PD (5 mm) at one year. Conclusions: In conclusion, within the limits of this retrospective analysis, it can be affirmed that this combined mechanical–chemical and regenerative decontamination therapy is effective in the treatment of peri-implantitis.