Food quality and safety impose significantly huge health and economic problems. Cocoa industry is highly valuable, and anything that compromises it is solution-centered to save such treasure. Mycotoxins are one of the problems encountering this industry in the pre- and postharvest production, and negatively affecting its revenues. Farmers are using different chemical substances to fight mycotoxins, but recently, many researches were done on introducing natural substances such as herbal oil combinations as potential controller of mycotoxins, as a step to enhance the ability of the crop to resist fungal infection and prevent mycotoxins production. This book chapter sheds light on the different types of cocoa beans, their chemical composition, health impacts, the different types of mycotoxins they could be infected with, and the various prevention techniques that could be applied.