Chitosan (CS) and its derivatives show antimicrobial properties. This is of interest in preventing and treating denture stomatitis, which can be caused by fungi. Therefore, the aim of this study was the development of a novel antifungal denture base material by modifying polymethyl methacrylate (PMMA) with CS-salt and characterizing its antifungal and surface properties in vitro. For this purpose, the antifungal effect of chitosan-hydrochloride (CS-HCl) or chitosan-glutamate (CS-G) as solutions in different concentrations was determined. To obtain modified PMMA resin specimens, the CS-salts were added to the PMMA before polymerization. The roughness of these specimens was measured by contact profilometry. For the evaluation of the antifungal properties of the CS-salt modified resins, a C. albicans biofilm assay on the specimens was performed. As solutions, both the CS-G and CS-HCl-salt had an antifungal effect and inhibited C. albicans growth in a dose-dependent manner. In contrast, CS-salt modified PMMA resins showed no significant reduced C. albicans biofilm formation. Furthermore, the addition of CS-salts to PMMA significantly increased the surface roughness of the specimens. This study shows that despite the antifungal effect of CS-salts in solution, a modification of PMMA resin with these CS-salts does not improve the antifungal properties of PMMA denture base material.