The study focuses on the development of a new family of layer-by-layer coatings comprising Nafion, lysozyme and chitosan to address challenges related to microbial contamination. Circular dichroism was employed to gain insights on the interactions of the building blocks at the molecular level. Quartz crystal microbalance tests were used to monitor in real time the build-up of multilayer coatings, while atomic force microscopy, contact angle and surface zeta potential measurements were performed to assess the surface characteristics of the multilayer assemblies. Remarkably, the nanocoated surfaces show almost 100% reduction in the population of both Escherichia coli and Staphylococcus aureus. The study suggests that Nafion based synergistic platforms can offer an effective line of defence against bacteria, facilitating antimicrobial mechanisms that go beyond the concept of exclusion zone.