ZnO nanoparticle-based multilayer nanocomposite films were fabricated on cationized woven cotton fabrics via layer-by-layer molecular self-assembly technique. For cationic surface charge, cotton fabrics were pretreated with 2,3-epoxypropyltrimethylammonium chloride (EP3MAC) by pad-batch method. XPS and SEM were used to examine the deposited nano-ZnO multilayer films on the cotton fabrics. The nano-ZnO films deposited on cotton fabrics exhibited excellent antimicrobial activity against Staphylococcus aureus bacteria. The results also showed that the coated fabrics with nano-ZnO multilayer films enhanced the protection of cotton fabrics from UV radiation. Physical tests (tensile strength of weft and warp yarns, air permeability and whiteness values) were performed on the fabrics before and after the treatment with ZnO nanoparticles to evaluate the effect of layer-by-layer (LbL) process on cotton fabrics properties.