Backround: The agr (accessory gene regulator) quorum sensing (QS) system of Staphylococcus aureus participates significantly in its virulence and biofilm formation—either through its activation or suppression. The aim of this study was to investigate the impact of photoactive nanomaterials that have been functionalized with erythrosine B (EryB) on the modulation of this agr QS system on three methicillin-resistant S. aureus (MRSA). Methods: The functionality of the agr system was determined by the CAMP test and by quantitative PCR (qPCR) to analyze the expression of the hld gene, which is located within the RNAIII and encodes δ-hemolysin. The biofilm was evaluated by crystal violet assay and fluorescence microscopy. The anti-biofilm activity was determined by calculating the colony-forming units. The relative expression of the hld gene, determined by qPCR. Results: Using the CAMP test, S66 and S68 strains were found to be agr-positive, and strain S73 was agr-negative. The relative expression of the hld gene increased only in the agr-positive strains (600- and 1000-fold). In these strains, the biofilm was less compact compared to the dense biofilm formed by the agr-negative strain. The anti-biofilm effectiveness on the nanocomposite with EryB after irradiation reduced the growth of biofilm cells by 100- to 1000-fold compared to the biofilm on polyurethane alone. The qPCR results showed a significant decrease in the relative expression of the hld gene in the agr-positive strains after irradiation compared to the non-irradiated samples. Conclusions: These results suggest that photoactive nanocomposites with EryB can significantly reduce biofilm formed by MRSA strains, regardless of the functionality of the agr QS system.