Essential oils (EOs) have been used for thousands of years. They are highly beneficial to human health due to their antioxidant and antimicrobial properties, besides protecting food from deterioration. This current study looks at the essential oils Origanum vulgare and Thymus vulgaris encapsulated in zein nanocapsules using the nanoprecipitation method with a non-ionic Pluronic surfactant. The encapsulation success of EOs was confirmed using transmission electron microscopy (TEM), scanning electron microscopy (SEM), dynamic light scattering (DLS), thermogravimetric analysis (TGA), and differential scanning calorimetry (DSC). EOS-loaded nanocapsules showed physical and chemical stability in storage (at 4 °C and 20 °C) for 90 days of monitoring with regard to antioxidant activity, encapsulation efficiency, polydispersion index, and zeta potential. The controlled release of nanoparticles is explained by the Korsmeyer–Peppas kinetic model. Nanocapsules have greater antimicrobial activity against gram-positive than gram-negative bacteria. The nanocapsules produced also presented high thermal resistance to baking processes, protecting the bread from the proliferation of moulds and yeasts.