Fusarium and mycotoxin contamination in cereal-based food is ubiquitous according to systematic review of the scientific documentation of worldwide mycotoxin contamination in cereal and their products between 2008 and 2018, thus representing food safety issue. Food processing is the last defense step to prevent mycotoxin contamination in foods for human consumption. Therefore, it is with great urgency to develop strategies to inhibit fungi growth and mycotoxin production during food processing. Recently, plant-based essential oils (EOs) have received considerable attentions in the food industry due to broad-spectrum of antifungal activities and inhibitory effect against mycotoxin biosynthesis. In this presentation, parameters that impact on the formation of EO-in-water nanoemulsions and functional properties including antifungal and mycotoxin inhibitory efficacy in vitro are discussed. Micro-malting process was selected to be as an example to testify the antifungal efficacy of proper-designed EO-in-water nanoemulsions. Results indicated that physically stable EO-in-water nanoemulsions can be fabricated by incorporating either ≥75 wt% of corn oil or ≥50 wt% of medium chain triacylglycerol (MCT) into EO before homogenization. In general, the mycotoxin inhibitory efficacy of EO was enhanced considerably in nanoemulsion form than bulk oil. Among all selected five EOs, thyme and clove oil-in-water nanoemulsions had the greatest antifungal and mycotoxin inhibitory activities. At last, clove oil-in-water nanoemulsions stabilized by three different emulsifiers (Tween 80, bovine serum albumin, quillaja saponins) were selected to apply in micro-malting process according to our germinative energy test of barley seeds. All clove oil-in-water nanoemulsions had the capability to inhibit fungal growth and DON production during the micro-malting process. Among the three emulsifiers, Tween 80-stablized clove oil nanoemulsion displayed largest reduction of mycotoxin and least flavor impact on the final malt. The overall project showed a great potential for utilization of EO-in-water nanoemulsion as antifungal agent and mycotoxin inhibitor in the food industry.