Periodontal diseases are highly prevalent oral conditions associated with severe complications in the oral cavity. These inflammatory diseases are caused by the oral microbiome and are influenced by several factors, such as aging, tobacco usage, systemic illness and inadequate oral hygiene. Plant-derived phytochemicals are extensively utilized in managing various periodontal diseases due to the presence of antioxidant, anti-inflammatory and antibacterial activities. Plant materials have shifted attention from conventional medicine to indigenous medicine. Solanum xanthocarpum is a medicinal herb found in India. It exhibits various pharmacological properties essential for periodontal disease prevention and management. The current work analyzes various pharmacological properties of S. xanthocarpum aqueous extract. The S. xanthocarpum extracts’ antioxidant, anti-inflammatory and anti-microbial properties were ascertained by DPPH assay, HRBC membrane stabilization assay and disk diffusion assay, respectively. S. xanthocarpum’s active phytochemical components were detected using gas chromatography−mass spectrometry (GC-MS) estimation. Furthermore, molecular docking and simulation analysis were conducted to determine the interaction between phytocompounds and the RgpB protein of Porphyromonas gingivalis. Phytocompounds possessing anti-microbial, antioxidant and anti-inflammatory properties were detected through GC-MS estimation. The molecular docking and simulation analysis revealed the inhibitory mechanisms of the phytocompounds Solasodine, Lupeol and Quercetin against arginine-specific gingipain RgpB protein. Insilico analysis revealed that Lupeol had the highest binding energy of −263.879 Kcal/mol among the phytocompounds studied, followed by Solasodine with a binding energy of −102.457 Kcal/mol and Quercetin with a binding energy of 33.6821 Kcal/mol. The study revealed that S. xanthocarpum has significant potential as an herbal remedy for preventing and treating periodontal diseases. This may facilitate drug development in the future.