Biofilms are potential reservoirs for pathogenic microbes leading to a significant challenge for food safety, ecosystems, and human health. Various micro-and nanoparticles have been experimentally evaluated to improve biofilm inactivation by targeted delivery of antimicrobials. However, the role of transport processes and reaction kinetics of these delivery systems are not well understood. In this study, a mechanistic modeling approach was developed to understand the targeted delivery of chlorine to an Escherichia coli biofilm using a novel bioaffinity-based yeast microparticle. Biofilm inactivation by this delivery system was numerically simulated as a combination of reaction kinetics and transport phenomena. Simulation results demonstrate that the targeted delivery system achieved 7 log reduction within 16.2 min, while the equivalent level of conventional free chlorine achieved only 3.6 log reduction for the same treatment time. These numerical results matched the experimental observations in our previous study. This study illustrates the potential of a mechanistic modeling approach to improve fundamental understanding and guide the design of targeted inactivation of biofilms using biobased particles.