Objectives: This randomized, placebo-controlled, double-masked clinical trial aimed to evaluate the clinical and microbiological efficacy of professional mechanical plaque removal (PMPR) with or without adjunctive application of piperacillin plus tazobactam gel in the treatment of peri-implant mucositis (PiM) for up to 6 months. Materials and Methods: The study included 31 patients with peri-implant mucositis (bleeding on probing (BoP) > 1 at at least one site at baseline, absence of peri-implant bone loss compared with a previous radiograph). After randomized assignment to test and control groups, patients received full-mouth supragingival scaling with or without piperacillin plus tazobactam gel. Clinical examination was performed at baseline and after 3 and 6 months, and a microbiological examination was performed at baseline and after 3 months. Results: After six months, both treatment modalities resulted in significant reductions and improvements in clinical parameters at the implant sites. Neither study group achieved a complete resolution of PiM (i.e., BoP ≤ 1 per implant). The number of implants with BoP decreased statistically significantly between subsequent time points (p < 0.001) in both the test and the control group. Significant BoP differences (p = 0.039) were observed between groups at 6 months (difference to baseline) following therapy. Conclusions: Within the limitations of the present study, the single use of a slow-release, locally applied antibiotic combination of piperacillin and tazobactam gel, adjunctive to PMPR, showed an improvement in clinical variable of implants diagnosed with PiM. The adjunctive treatment resulted in higher BoP reduction when compared to the control, but no significant differences were observed regarding the changes in other clinical and microbiological parameters.