This study assessed the efficacy of five denture cleansers on the microbial adherence and surface topography of conventional and CAD/CAM denture base resins. Acrylic resin discs were fabricated using conventional, milling, and 3D printing methods (N = 180). The discs were contaminated with dual species of Candida albicans and Streptococcus mutans biofilm for 72 h and then disinfected with either of the denture cleansers (Fittydent cleansing tablets, 2% Chlorhexidine gluconate, 0.2% Chlorhexidine gluconate, 0.5% sodium hypochlorite, and 1% sodium hypochlorite (n = 10). Distilled water served as the control group. The colony-forming units of the microorganisms were calculated, followed by post-treatment surface roughness. Data were statistically analyzed using one-way ANOVA, paired t-test, and post hoc Tukey HSD test (α = 0.05). Among the denture cleansers, 2% Chlorhexidine gluconate, 0.5% sodium hypochlorite, and 1% sodium hypochlorite had the best cleansing effect on the resin discs and demonstrated zero growth of colonies for both the species. Comparing the material groups, the 3D-processed discs showed higher colony-forming units followed by the conventional and CAD/CAM milled group. The highest surface roughness was demonstrated by the 3D-printed discs (0.690 ± 0.08 μm), followed by the conventional (0.493 ± 0.11 μm) and the milled groups (0.301 ± 0.08 μm). The tested chemical denture cleansers affected the Candida albicans and Streptococcus mutans adhesion compared to control discs immersed in distilled water. The clinician may recommend to their patient to use 2% chlorhexidine gluconate for the disinfection of CAD/CAM PMMA denture base materials.