Aims: In this study, benzalkonium chloride (BAC) microcapsules were developed for surface disinfection purpose and were evaluated against Listeria monocytogenes and Escherichia coli biofilms.Methods and Results: Microcapsules were prepared with two different strategies: uncomplexed BAC‐microcapsules (UBM), containing BAC and maltodextrins and complexed BAC‐microcapsules (CBM) containing BAC complexed by pectin and maltodextrins. The minimum inhibitory concentrations (MICs) of free and microencapsulated BAC was investigated against two food pathogens: L. monocytogenes and E. coli. The antibiofilm activities of UBM and CBM against L. monocytogenes and E. coli biofilms formed on stainless steel at 37°C were evaluated and compared to BAC used under its free form. MICs of encapsulated BAC were up to 4‐fold lower than those of free BAC. The UBM and CBM showed higher antibiofilm effect when compared to the free BAC.Conclusions: Overall, results demonstrated that microencapsulation enhanced the antibacterial activity of BAC against L. monocytogenes and E. coli biofilms.Significance and Impact of the Study: The application of such BAC microcapsule‐based delivery systems can improve surface disinfection procedures and reduce the required BAC concentrations and the related cytotoxicity of this antimicrobial compound.