Nowadays, antibiotics are the only therapeutic agents against Staphylococcus aureus infection. Widespread antibiotic resistance poses a threat to the world. Several studies have attempted to test whether alternative agents acting alone or in synergy with antibiotics can overcome this problem. For many years, silver nanoparticles have demonstrated multi-level action targeting the physiological activities of bacteria. The study aimed to synthesize silver nanoparticles by the green method from Acacia glauca leaves stabilized by chitosan (Ch-AgNPs) and evaluate their effect against the expression of a set of quorum sensing and virulent genes in MDR S. aureus. Ch-AgNPs were characterized by physicochemical tests including UV, X-ray, FTIR, TEM, FESEM, XRD, and zeta potential. Minimum inhibition concentration (MIC) was used to detect the antibacterial activity of Ch-AgNPs. After MIC treatment, the growth curve of S. aureus was plotted. The expression of genes (gyrb, AgrA, AgrB, RNAIII, mecA, rot, spa, hla, coa, and psm) was evaluated before and after exposure to Ch-AgNPs by quantitative real-time PCR. The dark brown color was the primary indicator of Ch-AgNPs formation. Ch-AgNPs showed absorption at 430 nm. The particles had a round and regular shape with an average size of 8 nm. The synthesized nanoparticles have a high degree of crystallinity, with thin peaks at 2θ° of 38.200 and 44.250. At +33 mV, the zeta potential confirmed high colloidal stability. The synthesized nanoparticles showed a high antibacterial effect with a MIC of 2.1 μg/mL, inhibiting the growth of S. aureus. All identified genes showed a significant decrease in their expression by RT-PCR after exposure to a subMIC of Ch-AgNPs, except for the gyrb gene, which is a housekeeping gene. Silver nanoparticles made from Acacia glauca leaves have the potential to be an effective antibacterial agent. They exert effects at a molecular level against the quorum sensing and virulence genes of MDR S. aureus.