AIM: This study investigates the mechanisms of action of a promising series of previously synthesized quaternary ammonium (QASs) and phosphonium (QPSs) salts, which have shown potent activity against Staphylococcus aureus, including methicillin-resistant strains (MRSA). METHODS AND RESULTS: The effects of QASs and QPSs on S. aureus surface charge, total surface hydrophobicity, intracellular potassium release, membrane integrity, and ultrastructure were examined. QASs and QPSs significantly altered bacterial surface properties by reducing negative surface charge, disrupting membrane integrity, and inducing potassium leakage and propidium iodide uptake. Furthermore, S. aureus became less hydrophilic due to changes in surface hydrophobicity. Transmission electron microscopy revealed cytoplasmic leakage and the presence of electron-dense extracellular material around damaged bacterial cells upon exposure to high concentrations of these salts. CONCLUSIONS: The antimicrobial activity of QASs and QPSs is driven by their ability to alter bacterial surface properties, destabilizing and disrupting membranes.