The linker-free covalent immobilization of polymers on surfaces has the potential to impart new properties and functions to surfaces for a wide range of applications. However, most current methods for the production of these surfaces involve multiple chemical steps and do not have a high degree of control over the chemical functionalities at the surface. A comprehensive study detailing the facile two-step covalent grafting of the antimicrobial peptide nisin onto polystyrene surfaces is reported. Functionalization is achieved using an atmospheric pressure plasma jet, and the reaction is monitored and compared with a standard wet chemical functionalization approach using a variety of analytical techniques. The reactive species produced by the atmospheric pressure plasma jet were analyzed by mass spectrometry and optical emission spectroscopy. The surface chemistry and topography of the functionalized surfaces were determined using contact angle measurements, Fourier infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy and atomic force microscopy respectively. Following surface analysis, the antimicrobial efficacy of the covalently grafted nisin against two major food borne pathogens (Staphylococcus aureus and Listeria monocytogenes) was assessed at two different pHs. The results demonstrated that a post-plasma treatment step after nisin deposition is required to covalently graft the peptide onto the surface. The covalent immobilization of nisin resulted in a significant reduction in bacterial counts within a short 30 minutes contact time. These surfaces were also significantly more antimicrobial compared to those prepared via a more traditional wet chemical approach indicating that the reported method could be a less expensive and less time consuming alternative.