Antimicrobial packaging can preserve and increase shelf life of free preservatives food products. Active materials present in the packaging material can migrate, in a controlled manner, to the food surface, avoiding bacterial and fungal proliferation and keeping the food product edible for longer periods of time. Essential oils (EO) are natural antimicrobial agents that can be released to the headspace with no direct contact between the package and the food. To minimize loses of EO during high heat melt processing, a three stages process was implemented and tested. Antimicrobial films were prepared by melt mixing a variety of polyethylene copolymers in the presence of organo-modified montmorillonite nano clay (NC) and thymol, an EO present in oregano and thyme. A controlled EO desorption from films can be achieved by changing the polymer crystallinity and polarity. As the crystallinity increased, the thermal stability of the EO during the extrusion process improved. The addition of NC affects the structure and homogeneity of the crystals. The combination of high polymer crystallinity and chemical affinity between EO and NC increased the thermal stability of the EO during film processing, enabling to control the desorption rate. The effect of multilayer structure based on varied densities and polarities was also studied. Increasing the polarity of the outer layers in multilayered film reduced the EO desorption rate as a result of chemical interactions between the polymer and the EO. The final antimicrobial activity of the films was also found to be dependent on the EO partitioning. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014, 131, 40309.