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The aim of this study was to evaluate the structural, physical, and antifungal characteristics of starch edible films added with nanocomposites and Mexican oregano (Lippia berlandieri Schauer) essential oil (EO). Starch edible films were formulated with Mexican oregano EO (0%, 1%, or 2% v/v) and bentonite or halloysite (2%). Physical properties such as L* (luminosity), hue, film thickness, and O2 and CO2 permeability were determined. Structural analysis was carried out via atomic force microscopy (AFM). Antifungal activity against Aspergillus niger, Fusarium spp., and Rhizopus spp. was evaluated. The addition of EO and nanocomposites reduced luminosity, providing color to the edible films. Film thickness increased through the addition of EO concentration. O2 and CO2 permeability was increased by bentonite/EO films, and for halloysite films, CO2 permeability decreased as EO concentration increased. The addition of EO with both nanocomposites shows an evident morphological change in film structure, decreasing pore density and increasing pore size. In general, Mexican oregano EO added to edible starch films has an adequate fungicidal effect. The most sensitive microorganism tested was A. niger. Edible films added with Mexican oregano EO and nanocomposites show better physical and antifungal properties due to an adequate structural change in the biopolymer matrix.