Nanoencapsulation may improve antimicrobial activity of nisin when applied on food systems such as lean beef. Nisin-loaded nanoparticles were prepared by alginate ionic gelation and further complexation with chitosan. A 3-factor, 3-level Box-Behnken experimental design and response surface methodology were used to optimize the formulation. Nanoparticles had an encapsulation efficiency of 36.1 ± 0.6%, a z-average of 66.4 ± 8.9 nm and a zeta potential of −31.7 ± 2.6 mV. Transmission electron microscopy and atomic force microscopy observations confirmed particle size found by dynamic light scattering. Also, Raman spectroscopy analyses and zeta potential measurements showed ionic interactions between nisin and alginate. In vitro assessment of inhibition of Listeria monocytogenes growth at 4 °C indicated sustained antimicrobial activity of nisin-loaded nanoparticles for 21 days. Furthermore, encapsulated nisin was able to inhibit L. monocytogenes growth in vacuum-sealed, refrigerated beef samples for 10 days when applied at 400 IU/g and for 24 days when applied at 800 IU/g, while free nisin controlled microbial growth for only 4 and 17 days respectively. In sum, we describe the application of experimental design tools to produce nisin-loaded nanoparticles that may be used in the food industry to control microbial growth and hence extend the shelf-life of lean beef.