This study aimed to test the efficacy of different silica-based toothpastes with or without chitosan, as a method of cleaning the acrylic surfaces of denture prostheses. Acrylic resin specimens were prepared to evaluate surface roughness and gloss (n = 10), and Candida albicans adhesion/inhibition (n = 2). Two toothpastes with different degrees of abrasiveness were used: Colgate (CT) and Elmex (EX), with or without 0.5% chitosan (Ch) microparticles (CTCh or EXCh, respectively). The negative control was brushed with distilled water. Brushing was simulated with a machine. Surface roughness and gloss were analyzed before and after brushing. Candida albicans incidence/inhibition was tested qualitatively to determine the acrylic resin antifungal activity. The roughness and gloss data were analyzed with a generalized linear model, and the Kruskal Wallis and Dunn tests, respectively (α = 5%). Brushing with toothpastes increased roughness and reduced gloss, compared with the negative control (p < 0.05). CT showed a more significantly different change in roughness and gloss, in relation to the other groups (p < 0.05). Addition of chitosan to CT reduced its abrasive potential, and yielded results similar to those of EX and EXCh. Specimens brushed with CT showed a higher potential for Candida albicans adherence, despite its higher antifungal action. Addition of chitosan to the toothpaste made both toothpaste and brushing more effective in inhibiting Candida albicans. CT had the potential to increase roughness, reduce gloss, and increase Candida albicans adherence. In contrast, chitosan added to CT showed greater antifungal potential, and a higher synergistic effect than EX.