Microbial biofilm is the primary cause of peri-implant mucositis, a reversible inflammatory illness affecting the soft tissues surrounding implants. Probiotics and other adjuvant therapies are becoming viable, physiologically sound alternatives to non-surgical mechanical debridement, which is the mainstay of care. To assess topically applied probiotic gel's supplemental clinical and microbiological benefits when used in conjunction with non-surgical mechanical debridement to treat peri-implant mucositis. Forty patients with peri-implant mucositis who were otherwise healthy were included in prospective clinical research. Participants were split into two groups at random: Group 1 underwent non-surgical mechanical debridement and placebo gel, whereas Group 2 underwent non-surgical mechanical debridement and topical application of probiotic gel once daily for two weeks. At baseline and six months later, clinical parameters (Plaque Index [PI] and Gingival Index [GI]) and microbial load (CFU/mL) were measured. SPSS Version 23.0 was used for the statistical analysis, and p < 0.05 was used for significance. Both groups exhibited significant within-group improvements. However, the probiotic group (Group 2) showed significantly greater reductions in PI (0.42 ± 0.03 vs 1.31 ± 0.09), GI (0.46 ± 0.03 vs 1.42 ± 0.09), and microbial load (0.64 ± 0.04 × 10² vs 1.12 ± 0.09 × 10² CFU/mL) compared to the control group (Group 1) at 6th month (p < 0.05). The clinical and microbiological results of non-surgical mechanical debridement in peri-implant mucositis are much improved by adjuvant topical probiotic treatment. This noninvasive method presents a viable supplement to evidence-based peri-implant therapy.