The aim of this study was to evaluate and compare two different one-stage full-mouth disinfection protocols in the treatment of chronic periodontitis by assessing dental plaque and tongue coat using BANA assay. The present study was a prospective randomized clinical parallel arm study design including 40 healthy subjects randomly allocated into two groups, i.e., group A (Quirynen's protocol of one-stage full-mouth disinfection) and group B (Bollen's protocol of one-stage full-mouth disinfection). Subjects were assessed at baseline and six weeks using plaque index, gingival index, and sulcus bleeding index. Probing depth and relative clinical attachment level were also recorded at six weeks. Winkel tongue coat index and BANA were recorded at 8 weeks using subgingival plaque and tongue coat sample. Both group A and group B demonstrated statistically significant reduction in plaque index, gingival index, sulcus bleeding index, Winkel tongue coat index, reduction in probing depth, and gain in relative clinical attachment level on intragroup comparison. There was no significant difference in BANA assay score of subgingival plaque and tongue coat samples in between group A and group B. From the findings of this study, both Quirynen's protocol and Bollen's protocol of one-stage full-mouth disinfection are effective in plaque reduction and tongue coat reduction and achieve comparable clinical healing outcomes. The difference in duration and mode of use of chlorhexidine as a chemical plaque control agent in the two treatment interventions of Quirynen's and Bollen's protocol of one-stage full-mouth disinfection did not demonstrate statistical significance in reducing sulcus bleeding index scores, reducing probing depths, and gain in relative clinical attachment levels.