When exposed to different types of bacteria in the oral cavity, denture based resins are prone to bacteria attachment. The purpose of this study was to investigate the physical, biological, and antimicrobial properties of denture base resins coated with Peony extract (200, 400, and 600 μg/mL). Specifically, the surface properties (microhardness, contact angle, and color change of the coated specimens), cell cytotoxicity (measured using MTT assay), and antimicrobial activity (against S. mutans (Streptococcus mutans) and C. albicans (Candida albicans) using a growth inhibition assay) were evaluated. The polyphenol content was measured using ultraviolet-visible (UV-vis) spectrometry. The experimental groups (specimens coated with Peony extract) and a control group (specimens coated without Peony extract) were statistically compared using a one-way analysis of variance and Tukey’s post-hoc tests. No statistically significant differences in surface properties or cell cytotoxicity were observed, which demonstrated their biocompatibility. Conversely, a statistically significant difference in antimicrobial activity was observed between the experimental and control groups after 48 h. This confirms the antimicrobial activity of the denture base resin coated with Peony extract and demonstrates that it is a promising dental material for preventing stomatitis.