Deoxynivalenol (DON) is a commonly occurred mycotoxin in cereal-based food, which is mainly produced by Fusarium spp. in the field. It is unfeasible to entirely avoid DON contamination in cereal grains with good agricultural practices. Therefore, it is of great importance to have a strategy for preventing DON contamination in our final food products. In recent years, utilization of plant extracts such as essential oils (EOs) as antifungal and mycotoxin inhibitory agents in foods have gained popularity. Depending on the EO type and chemical composition of EOs, the antifungal and mycotoxin inhibitory efficacies of different EOs might be varied. In addition, their antifungal mode of actions (MOA) against Fusarium spp. growth remains unknown. Therefore, the overall objectives of this project were to understand how different type of clove EOs (clove bud EO and clove leave EO), hop essential oil (HEO) impact their antifungal and mycotoxin inhibitory efficacies, and their corresponding antifungal MOA. Finally, HEO in nanoemulsion form was applied to evaluate their application during micro malting process using naturally Fusarium infected barley grains. Results denoted that physically stable 5 wt% EO in-water nanoemulsions with the mean particle sizes less than 170 nm can be built by blending either corn oil or medium chain triglyceride (MCT) with EOs. The largest percentage of chemical constituent in clove essential oils (CO) and HEO was eugenol (phenol type) and β-myrcene (monoterpene type), respectively. In terms of their application as antifungal agents, CO had better antifungal and mycotoxin inhibitory efficacy against Fusarium graminearum growth and DON production in vitro as compared to HEO because of their high percentage of eugenol content. The major antifungal MOA of EO nanoemulsions included altering total lipid content in cell, chitin content in outer spore cell membrane, and damaging cytoplasmic membrane. In the application case study, results indicated that Fusarium biomass (Tri 5 DNA) and DON contents were reduced at each malting stage with the treatments of HEO nanoemulsion by malting Fusarium infected barley. This study provided the valuable information on utilization of EO nanoemulsions as natural antifungal agents during food processing.