Oral diseases are often associated with bacterial and fungal pathogens such as Staphylococcus aureus, Streptococcus mutans, Enterococcus faecalis, and Candida albicans. This research explored a novel approach to addressing these pathogens by synthesizing zinc oxide nanoparticles (ZnO NPs) coated with rutin (RT), a plant-derived compound. The synthesized ZnO-RT NPs were comprehensively characterized using UV-Vis spectrophotometer, SEM, and EDAX techniques to confirm their structural composition. The antioxidant potential was assessed through free radical scavenging assays. Additionally, the antimicrobial activity of ZnO-RT NPs was evaluated using a zone of inhibition assay against oral pathogens. Molecular docking studies with the Autodock tool were performed to elucidate the interactions between RT and the receptors of oral pathogens. The findings demonstrated that ZnO-RT NPs exhibited robust free radical scavenging activity. Furthermore, they showed significant antimicrobial activity with a minimal inhibitory concentration of 40 μg/mL against oral pathogens. ZnO-RT NPs also displayed dose-dependent anticancer effects on human oral cancer cells at concentrations of 10, 20, 40, and 80 μg/mL. Mechanistic insights into the anticancer activity on KB cells revealed the upregulation of apoptotic genes. This study underscores the promising potential of ZnO-RT NPs for dental applications due to their strong antioxidant, anticancer, and antimicrobial properties. These nanoparticles offer a hopeful prospect for addressing oral pathogen challenges and enhancing overall oral health.