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<i>Background and Objectives</i>: To investigate the antiplaque properties of two plant-based mouthwashes, <i>Morinda citrifolia</i> (MC) and <i>Ocimum sanctum</i> (OS), and their effect on TNF-α, IL-α, IL-β, IL-2, and IL-6 in gingival crevicular fluid (GCF) of patients undergoing fixed orthodontic treatment. <i>Materials and Methods</i>: Seventy-five individuals were recruited according to defined inclusion and exclusion criteria. This study was structured into two distinct phases. Phase I was a combination of toothbrushing using toothpaste containing fluoride (Protocol A), while Phase II toothbrushing included fluoride toothpaste and use of a mouthwash (Protocol B). For Phase II, individuals participating in this study were allocated into different groups through a randomization process: Group 1—0.12% CHX, Group 2—5% MC, and Group 3—4% OS. Each individual’s Phase I and Phase II scores were assessed. GCF was measured in three phases to determine the level of inflammatory biomarkers. The paired <i>t</i>-test evaluated the disparities between the pre- and post-plaque index. Categorical data were subjected to crosstab analysis to assess qualitative variables. The mean values of cytokine levels were presented. An unpaired <i>t</i>-test was employed to assess the levels of cytokines between individuals in Phase I and Phase II. <i>Results</i>: Toothbrushing, fluoride toothpaste, and the supplementary use of mouthwash (Phase II) resulted in mean plaque scores significantly lower than group A (<i>p</i> < 0.001). Cytokines TNF-α, IL-α, and IL-β demonstrated a significant downward trend in herbal mouthwash users. <i>Conclusions</i>: In conjunction with fluoridated toothpaste and brushing, OS and MC can serve as a viable alternative to conventional synthetic mouthwash CHX. This combination demonstrates reducing mean plaque scores and diminishing the levels of cytokines TNF-α, IL-α, and IL-β.