The global turn from the linear to the circular economy imposes changes in common activities such as food packaging. The use of biodegradable materials such as polyvinyl alcohol, natural raw materials such as clays, and food byproducts such as chitosan to develop novel food packaging films attracts the interest of industrial and institutional research centers. In this study, novel hybrid nanostructures were synthesized via the growth of zinc oxide nanorods on the surface of two nanoclays. The obtained nanostructures were incorporated with chitosan/polyvinyl alcohol composite either as nanoreinforcement or as an active agent to develop packaging films. The developed films were characterized via XRD, FTIR, mechanical, water-vapor diffusion, water sorption, and oxygen permeability measurements. Antimicrobial activity measurements were carried out against four different pathogen microorganisms. XRD indicated the formation of an intercalated nanocomposite structure for both types of nanoclays. Furthermore, improved tensile, water/oxygen barrier, and antimicrobial properties were recorded for all films compared to the pure chitosan/polyvinyl alcohol film. Overall, the results indicated that the use of the bio-based developed films led to an extension of food shelf life and could be used as novel active food packaging materials. Among them, the most promising film was the 6% wt. ZnO@halloysite.