Mycotoxins 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 especially in developing tropical countries. Food processing plays a vital role to prevent mycotoxin contamination in food. Therefore, it is with great urgency to develop strategies to inhibit fungi growth and mycotoxin production during food processing. This review begins by discussing physicochemical properties of five most common mycotoxins (aflatoxins, fumonisins, ochratoxins, deoxynivalenol, and zearalenone) found in cereal grains, regulation for mycotoxins in food, and their potential negative impact on human health. The fate of mycotoxins during major cereal-based food processing including milling, breadmaking, extrusion, malting, and brewing was then summarized. In the end, traditional mitigation strategies including physical and chemical and potential application of biocontrol agent and essential oil nanoemulsions that can be applied during food processing were discussed. It indicated that no single method is currently available to completely prevent mycotoxin contamination in cereal foods.