Nuts, oilseeds and legumes are important dietary constituents to combat chronic diseases of lifestyle due to the presence of important dietary macro- and micronutrients. However, many potential hazards associated with the harvesting, storage and processing occur of which mycotoxin contamination appears to be one of the major causes for economic losses of foodstuff and health-related risks resulting in many animal and human diseases. The major toxigenic fungal genera are Aspergillus, Penicillium and Fusarium, producing a diverse group of mycotoxins with adverse toxicological effects of which the aflatoxins, ochratoxin A, deoxynivalenol, zearalenone and the fumonisins are some of the most common and well-researched mycotoxins. The levels of these mycotoxins, among others, are well controlled in food and feed in developed countries, whereas their regulation in developing countries is poor or lacking. Mycotoxin control in food commodities involves a range of interventions to secure safe food based on a farm to fork approach, including good agricultural, storage and processing practices, which form part of the Hazard Analysis Critical Control Points (HACCP) system. For example, pistachio nuts are associated with a high risk for pre-harvest aflatoxin contamination due to insect damage and “early splitting” of the fruit hulls, as well as during the extensive post-harvest processing of the nuts. The generic example of an HACCP plan for pistachio processing identifies five Critical Control Points (CCPs) which need careful monitoring to ensure a consumer product which adheres to international aflatoxin regulations. These CCPs include steps related to the use of flotation tanks, adequate removal of hull debris from the nut shells, proper drying and sorting prior to packaging or export. Key to this HACCP plan is good communication between pistachio producer and processor. These and other control parameters to reduce mycotoxin contamination are critically reviewed in the current chapter which will be important in food safety management regarding the control of mycotoxin exposure.