Background: The aim of this study, a prospective case series, was to evaluate the clinical, microbiological, and biochemical impact of the surgical treatment of peri-implantitis. Methods: Thirty subjects with diagnosis of peri-implantitis were treated following a surgical protocol including access flaps, surface decontamination with ultrasonics and glycine powder air-polishing, and systemic antibiotics. Disease resolution was defined by the composite outcome including presence of probing depths (PD) ≤5 mm, absence of bleeding on probing (BoP)/suppuration, and no additional radiographic bone loss (>1 mm). Regression analysis was used to evaluate the patient-, implant-, and prosthetic-related factors possibly influencing treatment outcomes. Results: Patients were evaluated at 6 months post treatment, demonstrating statistically significant reductions in PD (2.14 ± 1.07 mm) and increase in mucosal recession (1.0 ± 0.77 mm). Plaque, BoP, and suppuration were also reduced by 40.56%, 62.22%, and 7.78%, respectively. Disease resolution was achieved in 56.67% of patients. No significant changes were detected in microbiological parameters except for a significant reduction in proportions of Parvimonas micra. Similarly, the levels of the biomarker interleukin-8 in crevicular fluid were significantly lower at 6 months. Conclusions: The proposed surgical treatment of peri-implantitis demonstrated statistically significant clinical improvements although the impact on microbiological and biochemical parameters was scarce.