Nisin-loaded amaranth protein isolate:pullulan (API:PUL) nanofibers were prepared by the electrospinning method. The nisin release kinetic was evaluated at pH 3.4 and 6.1 and the antimicrobial effectiveness of the electrospun mats was evaluated in apple juice and fresh cheese. The nisin API:PUL fibers with 120 nm average diameter reached 81.49% and 43.85% nisin release after 12 h at pH 3.4 and 6.1, respectively. The encapsulation of nisin in electrospun fibers allowed complete bactericidal activity against Salmonella Typhimurium, L. monocytogenes and L. mesenteroides inoculated in apple juice after 48, 20 and 48 h, respectively. When nisin API:PUL fibers were applied to fresh cheese, microorganism inactivation was complete after 142, 120 and 170 h, respectively. The results demonstrated that nisin API:PUL electrospun fibers significantly reduce the bacterial population and can be used in food products for microbiological safety.