The interest in using natural antimicrobials instead of chemical preservatives in food products has been increasing in recent years. In regard to this, essential oils—natural and liquid secondary plant metabolites—are gaining importance for their use in the protection of foods, since they are accepted as safe and healthy. Although research studies indicate that the antibacterial and antioxidant activities of essential oils (EOs) are more common compared to other biological activities, specific concerns have led scientists to investigate the areas that are still in need of research. To the best of our knowledge, there is no review paper in which antifungal and especially antimycotoxigenic effects are compiled. Further, the low stability of essential oils under environmental conditions such as temperature and light has forced scientists to develop and use recent approaches such as encapsulation, coating, use in edible films, etc. This review provides an overview of the current literature on essential oils mainly on antifungal and antimycotoxigenic but also their antibacterial and antioxidant activities. Additionally, the recent applications of EOs including encapsulation, edible coatings, and active packaging are outlined.