Queso Fresco (QF), a widely produced Hispanic-style fresh cheese, is known to support the growth of Listeria monocytogenes. Nisin is a biopreservative with antimicrobial activity against L. monocytogenes; however, it has limited stability in near neutral pH foods, such as QF. The objective of this study was to evaluate the efficacy of nisin microencapsulated in zein against L. monocytogenes in QF. Zein microcapsules with low (LNM) and high (HNM) nisin loading (3–5 and 12–13 µg nisin/mg microcapsules, respectively) were prepared with a microfluidic device and nisin concentration was quantified via HPLC. Microencapsulated and free nisin were added to QF at a final concentration of 250 µg of nisin/g of cheese, and untreated cheeses were included as a control. The antilisterial activity of microencapsulated and free nisin was tested by inoculating cheese curds with approximately 4 Log cfu/g of L. monocytogenes cocktail of 5 different foodborne outbreak-associated strains, and L. monocytogenes cells were enumerated by spread plating on PALCAM agar supplemented with ceftazidime, across 7 d of storage at 4°C. All experiments were repeated 3 times with samples prepared in duplicate. Free nisin reduced the viable cell count of L. monocytogenes by approximately 0.8 Log cfu/g after 3 d, but subsequent regrowth led to a final population comparable to untreated QF. All treatments with nisin-loaded zein microcapsules achieved overall lower viable cell counts relative to free nisin, notably at early cheese storage. HNM reduced the initial viable population of L. monocytogenes by up to 1.5 Log cfu/g after 3 d. LNM showed higher viable pathogen reduction relative to HNM, reducing up to approximately 2 Log cfu/g from the initial inoculum after 7 d of cold storage. In conclusion, our results support the use of encapsulation technology to improve nisin’s effectiveness to control Listeria in QF.