Background: Denture stomatitis (DS) is a chronic mucosa inflammation that supports removable dentures. Candida albicans is the most critical factor in the pathogenesis of DS. Systemic antifungal drugs such as nystatin are effective in people with acute candidiasis. Yet, in cases of predisposing factors such as a denture, nystatin cannot completely control the infection, and recurrences are common. Objectives: In this study, the resistance and sensitivity of oral C. albicans species to nystatin were evaluated, and the effect of silver nanoparticles (AgNPs) was investigated on the nystatin-resistant specimens. Methods: This in vitro study was performed on 20 C. albicans specimens isolated from patients with denture stomatitis. After confirmation of C. albicans and in vitro biofilm preparation, nystatin was applied to the biofilm. The results were recorded as minimum growth inhibitory concentration (MIC) using Clinical & Laboratory Standards Institute (CLSI) standard protocol, and the specimens with MIC of more than 1 µg/mL were categorized as resistant. Then, biofilms were re-formed for nystatin-resistant specimens exposed to AgNPs, and MIC results were reported. Results: This study revealed that 8 C. albicans specimens (40%) represented a MIC of more than 1 µg/mL when exposed to nystatin. The results of AgNPs exposure to this group showed significantly higher efficiency of AgNPs than nystatin (P < 0.05). AgNPs can reduce the MIC of 6 nystatin-resistant specimens (75% of all resistant specimens). Conclusions: Both nystatin and AgNPs are effective against Candida biofilms formed on denture surfaces. However, AgNPs seem more effective in the case of resistant species.