Objectives Dysbiosis of oral microbiome play an integral role in periodontitis. Bacterial balance is an important aspect of host defence. Mechanical debridement alone is insufficient to manage many cases. Probiotics are a novel adjunctive strategy, but the beneficial effects of probiotics in the management of moderate periodontitis have not been evaluated before. The objective of the present study was to assess the efficacy of probiotic mouth rinse of Lactobacillus acidophilus, Lactobacillus rhamnosus, Bifidobacterium longum and Saccharomyces boulardii as an adjunct to mechanical debridement in grade II periodontitis. The study also evaluated change in salivary pH and IgA in both groups. Methods The study was registered under Clinical Trial Registry of India (CTRI NO: CTRI/2019/10/021630). 60 patients with stage II periodontitis were randomized into probiotic and placebo group (n = 30 in each group) after mechanical debridement. Patients were instructed to use mouth rinse twice a day for 30 days. Periodontal parameters (Plaque index, Gingival index, Pocket depth and clinical attachment level) were recorded at baseline, after 1 and 3 months. Salivary pH was tested using a pH metre and IgA using enzyme linked immunosorbent assay. Results Significant improvement in all clinical parameters were noted in both the groups after 1 and 3 months. Intergroup comparison revealed significant difference in gingival index, probing depth and clinical attachment gain. Significant elevation of salivary IgA and pH was noticed in probiotic group in contrast to placebo group. Conclusion The present study supports the use of probiotic mouthwash as an adjunct to mechanical therapy for the management of stage II periodontitis.