Unravelling the mechanisms of action of disinfectants is essential to optimize dosing regimes and minimize the emergence of antimicrobial resistance. In this work, we decipher the mechanisms of action of a commonly used disinfectant - benzalkonium chloride (BAC)- over a major pathogen -L. monocytogenes- in the food industry. For that purpose, we use modeling at multiple scales, from the cell membrane to the cell population inactivation. Molecular modeling reveals that the integration of the BAC into the membrane requires three phases: (1) the BAC approaches the cellular membrane, (2) the BAC is adsorbed on its surface, and (2) it is rapidly integrated into the lipid bilayer, where it remains at least for several nanoseconds, probably destabilizing the membrane. We hypothesize that the equilibrium of adsorption, although fast, is limiting for sufficiently large BAC concentrations, and a kinetic model is derived to describe kill-curves of a large population of cells. The model is tested and validated with time-series data of free BAC decay and time-kill curves of L. monocytogenes at different inocula and BAC dose concentrations. The knowledge gained from the molecular simulation plus the proposed kinetic model offers the means to rationally design novel disinfection processes.