This randomized, controlled, double-blinded clinical trial aimed to evaluate the efficacy of octenidine hydrochloride and chlorhexidine mouthwashes as adjuncts to instrumentation in stage I-II periodontitis patients. Forty-five patients with mild-to-moderate periodontitis were randomly allocated to three groups: 0.1% octenidine dihydrochloride (OCT), placebo, and 0.12% chlorhexidine (CHX) mouthwashes. Patients were instructed to use the mouthwash after instrumentation for twice a day up to 3 weeks. Periodontal parameters such as probing pocket depth (PPD), clinical attachment loss (CAL), O'Leary plaque index (PI), Loe and Silness gingival index (GI), Lobene stain index (SI), and oral soft tissue changes were recorded at baseline and once every week for 3 weeks. The visual analogue scale (VAS) was also recorded as a self-administered questionnaire at the end of the study. The one-way ANOVA was used to compare VAS scores between the groups. The repeated measures ANOVA and post hoc Newman-Keuls tests were used to assess the differences in the periodontal parameters between groups at different time intervals. The Kruskal-Wallis test was used to compare the mean SI. There was a significant reduction in the mean GI of the OCT and CHX groups compared to placebo (p < 0.05). OCT usage resulted in significantly less staining, according to mean SI, when compared to CHX. Furthermore, VAS scores revealed that OCT was significantly the preferred mouthwash (p < 0.01). Adjunctive octenidine hydrochloride may be an alternative to chlorhexidine in its ability to control the periodontal parameters in patients with stage I-II periodontitis. Further larger studies are necessary to confirm these findings.