The purpose of this study was to examine the anti-oral microorganism effects of fluorine and/or silver ions implanted into acrylic resin (PMMA) using plasma-based ion implantation (PBII) with argon gas. The experimental PMMA specimens were implanted with F and Ag ions alone or simultaneously by the PBII method using Ar or Ar/F2 gases and Ag mesh. The surface characteristics were evaluated by X-ray photoelectron spectroscopy (XPS), contact angle measurements, and atomic force microscopy (AFM). Moreover, the antibacterial activity against Streptococcus mutans (S. mutans) and the antifungal activity against Candida albicans (C. albicans) were examined by the adenosine-5’-triphosphate (ATP) emission luminescence method. XPS spectra of the modified specimens revealed peaks due to F in the Ar/F and the Ar/F+Ag groups, and due to Ag in the Ar+Ag and the Ar/F+Ag groups. The water contact angle increased significantly due to the implantation of Ar, F, and Ag. In the AFM observations, the surface roughness of the Ar/F and the Ar/F+Ag groups increased significantly by less than 5 nanometers. The presence of F and Ag was found to inhibit S. mutans growth in the Ar+Ag and the Ar/F+Ag groups. However, this method provided no significant antifungal activity against C. albicans.