Aim: To investigate the antifungal activity of two different functionalized gold nanoparticles (AuNP), those stabilized with cetyltrimethylammonium bromide and those conjugated with cysteine, and their effects on the architecture of Candida tropicalis biofilms. Materials & methods: Biofilms were studied by crystal violet binding assay and scanning electron microscopy. We investigated the effects of AuNPs on reactive oxygen species, reactive nitrogen intermediates and enzymatic and nonenzymatic antioxidant defenses. Results/Conclusion: The fungicidal activity and cellular stress of both AuNPs affected biofilm growth through accumulation of reactive oxygen species and reactive nitrogen intermediates. However, cetyltrimethylammonium bromide-stabilized AuNPs revealed a higher redox imbalance. We correlated, for the first time, AuNP effects with the redox imbalance and alterations in the architecture of C. tropicalis biofilms.