Introduction: Oral diseases are common diseases that occur frequently and are estimated to affect half of the global population. The occurrence and development of most oral diseases are closely associated with oral microbiome. Methodology: Individuals with gingivitis and the early stages of periodontitis participated in a 2-month comparative clinical study comparing toothpaste with 1450 ppm sodium monofluorophosphate and xylitol (the control; 15 patients) and tooth paste containing further botanical extracts (the experiment; 35 patients). The Loe & Silness, CPITN, OHI-S, and PMA indices were used to measure the clinical indicators of gingivitis and periodontitis. In the gingival crevicular fluid and plaque, the pro-inflammatory and anti-inflammatory interleukins, nitrites/nitrates, total antioxidant activity, and bacterial distribution typical of gingivitis and periodontitis were measured. Results: Clinically speaking, experimental toothpaste was more effective in reducing the bacterial load specifically associated with gingivitis/periodontitis. Herbal extracts had anti-inflammatory, anti-oxidant, direct, and indirect anti-bacterial activities through inhibition of bacterial defence versus phagocytes, whereas the control toothpaste had a modest direct anti-bacterial impact. Conclusions: Due to their various modes of action, chemical and plant-derived anti-bacterials should be used in conjunction to treat gingivitis and periodontitis at their early stages. Due to their numerous beneficial impacts, plant-derived active ingredients for oral care could replace hazardous chemicals.