The use of natural compounds with biocidal activity to fight the growth of bacteria responsible for foodborne illness is one of the main research challenges in the food sector. This study reports the preparation and physicochemical characterization of chitosan nanoparticles loaded with Thymus capitatus (Th-CNPs) and Origanum vulgare (Or-CNPs) essential oils. The nanosystems were obtained by ionotropic gelation technique with high encapsulation efficiency (80–83%) and loading capacity (26–27%). Nanoparticles showed a spherical shape, bimodal particle size distribution, and good stability (zeta potential values > 40 mV). The treatment of the nanosuspensions at different temperatures (4 and 40 °C) and storage times (7, 15, 21, and 30 days) did not affect their physicochemical parameters and highlights their reservoir ability for essential oils also under stressful conditions. Both Or-CNPs and Th-CNPs exhibited an enhanced bactericidal activity against foodborne pathogens (S. aureus, E. coli, L. monocytogenes) than pure essential oils. These ecofriendly nanosystems could represent a valid alternative to synthetic preservatives and be of interest for health and food safety.