We comprehensively profiled intracellular and ECM proteomes of S. aureus flow biofilms and complemented these data by metabolic footprint analysis and phenotypic assays. We show that S. aureus biofilms produce high amounts of secreted, moonlighting virulence factors stabilizing the ECM. Mechanistically, we propose that these alkaline virulence factors get protonated in an acidified ECM (due to the release of acids upon fermentation) mediating electrostatic interactions with anionic cell surface components and metabolites, which leads to cell aggregation and ECM stabilization.