The global demand for safe and healthy food with minimal synthetic preservatives is continuously increasing. Natural food antimicrobials and especially essential oils (EOs) possess strong antimicrobial activities that could play a remarkable role as a novel source of food preservatives. Despite the excellent efficacy of EOs, they have not been widely used in the food industry due to some major intrinsic barriers, such as low water solubility, bioavailability, volatility, and stability in food systems. Recent advances in nanotechnology have the potential to address these existing barriers in order to use EOs as preservatives in food systems at low doses. Thus, in this review, we explored the latest advances of using natural actives as antimicrobial agents and the different strategies for nanoencapsulation used for this purpose. The state of the art concerning the antibacterial properties of EOs will be summarized, and the main latest applications of nanoencapsulated antimicrobial agents in food systems will be presented. This review should help researchers to better choose the most suitable encapsulation techniques and materials.