The aim of this work is the encapsulation of essential oils (EOs) in polymeric nanocapsules (NCs), in order to enhance their antimicrobial activity against food-borne pathogens. Thymus capitatus and Origanum vulgare EOs were selected for their different chemical composition, carvacrol (73%) and thymol (44%) being the major constituent, respectively. Polymeric poly(ɛ-caprolactone) (PCL) nanocapsules loaded with EOs were prepared by a nanoprecipitation method. The EO-NCs showed monomodal distribution with diameter size 171 and 175 nm, high efficiency of encapsulation and stability with high retention of EOs at both 4 °C and 40 °C, for a period of at least 30 days. The antimicrobial activity of EO-NCs against food-borne pathogens was higher than that of the corresponding pure essential oils and the NCs loaded with Thymus capitatus EO were the most active. Interestingly EO-NCs showed a …