Numerous studies have been reported to encapsulate drugs or other bioactive compounds in biopolymeric micro- or nanocapsules to achieve a controlled release of the bioactives. Food biopolymers are less studied as carriers, albeit abundant and generally-recognized-as-safe. Further, many of the processes used to encapsulate bioactives are questionable for food applications that require very large production capacities and appropriate solvents. This work reports release characteristics of lysozyme, a naturally-occurring antimicrobial, from corn zein microcapsules produced using spray drying. We show that the additives of surfactant and essential oil profoundly changed the internal structures of capsules and that nanostructures of these capsules controlled the mass transfer of the encapsulated lysozyme. Without additives, micrometer-sized pores existed in microcapsules, which corresponded to quick equilibria of lysozyme release profiles at pH 2-8, with a smaller amount of lysozyme released at a higher pH. With the addition of Tween 40, the release characteristics was not fundamentally changed, although the matrix of microcapsules changed to packed nanoparticles. When thymol was used, the wall structure became continuous at the nanoscale observed and a sustained release was observed at pH 6 and 8 over 36 days. This work illustrated that molecular interactions and nanoscale structures both determined release profiles of lysozyme. The technology being developed may be used to produce food grade antimicrobial delivery systems to enhance microbial food safety.