This study aimed to evaluate the influence of denture cleansers on the color, stability, and surface roughness of three-dimensional (3D)-printed denture base resins modified with zirconium dioxide nanoparticles (nano-ZrO2). A total of 440 specimens were fabricated using one heat-polymerized resin, and two 3D-printed resins (NextDent and ASIGA). According to the nano-ZrO2 content, the specimens for each resin were divided into five groups (0%, 0.5%wt, 1%wt, 3%wt, and 5%wt). Each concentration was divided into four subgroups (n = 10) based on the immersion solution (distilled water, sodium hypochlorite, Corega, and Fittydent) and immersion duration (360 and 720 days). The color changes (∆E00) and surface roughness (Ra, µm) of each specimen were measured at different time intervals (base line, 360 days, 720 days) using a spectrophotometer and a non-contact profilometer, respectively. The results were statistically analyzed using ANOVA and a post hoc Tukey’s test (α = 0.05). Sodium hypochlorite showed the highest significant color change of all the denture base resins (p < 0.001). The average value of ΔE00 for sodium hypochlorite was significantly higher than the values for the other solutions (Fittydent, Corega, and water) (p < 0.001). Color stability was significantly affected by immersion time for all types of solutions except Corega (p < 0.001). All of the tested immersion solutions (distilled water, sodium hypochlorite, Corega, and Fittydent) showed a significant increase in the surface roughness of all the denture base resins (p < 0.05). Surface roughness was substantially increased by immersion time for all types of solution except Fittydent (p < 0.001). Denture cleansers can result in substantial color change and affect the surface roughness of unmodified and nanoparticle-modified denture base resins. Therefore, the selection of denture cleanser and appropriate types of material is critical for denture longevity.