An antimicrobial polymeric bilayer structure based on the application of an acrylic coating containing hollow zinc oxide nanotubes over a polymeric substrate was developed in this work. Firstly, zinc oxide nanotubes (ZnONT) were obtained by an atomic layer deposition (ALD) process over electrospun polyvinyl alcohol nanofibers followed by polymer removal through calcination with the purpose of obtaining antimicrobial nanostructures with a high specific area. Parameters of electrospinning, ALD, and calcination processes were set in order to obtain successfully hollow zinc oxide nanotubes. Morphological studies through scanning electron microscopy (SEM) and transmission electron microscopy (TEM) microscopies confirmed the morphological structure of ZnONT with an average diameter of 180 nm and thickness of approximately 60 nm. Thermal and X-ray diffraction (XRD) analyses provided evidence that calcination completely removed the polymer, resulting in a crystalline hexagonal wurtzite structure. Subsequently, ZnONT were incorporated into a polymeric coating over a polyethylene extruded film at two concentrations: 0.5 and 1 wt. % with respect to the polymer weight. An antimicrobial analysis of developed antimicrobial materials was performed following JIS Z2801 against Staphylococcus aureus and Escherichia coli. When compared to active materials containing commercial ZnO nanoparticles, materials containing ZnONT presented higher microbial inhibition principally against Gram-negative bacteria, whose reduction was total for films containing 1 wt. % ZnONT. Antiviral studies were also performed, but these materials did not present significant viral reduction.