The fate of aflatoxins and fumonisins, two mycotoxins that cooccur in maize, was studied through the traditional processing of naturally contaminated maize in mawe, makume, ogi, akassa, and owo, maize-based foods common in Benin, West Africa. Levels of total aflatoxin and fumonisin were measured at the main unit operations of processing, and the unit operations that induce significant reduction of mycotoxin level were identified. Overall reduction of mycotoxin level was more significant during the preparation of makume (93% reduction of aflatoxins, 87% reduction of fumonisins) and akassa (92% reduction of aflatoxins, 50% reduction of fumonisins) than that of owo (40% reduction of aflatoxins, 48% reduction of fumonisins). Sorting, winnowing, washing, crushing combined with dehulling of maize grains were the unit operations that appeared very effective in achieving significant mycotoxin removal. Aflatoxins and fumonisins were significantly recovered in discarded mouldy and damaged grains and in washing water. Fermentation and cooking showed little effect. During the preparation of ogi and akassa, reduction of fumonisin levels measured in food matrix was lower (50%) compared to mawe and makume, probably due to significant fumonisin release in ogi supernatant. Consequently, the use of ogi supernatant for preparing beverages or traditional herbal medicines could be harmful as it is likely to be contaminated with mycotoxin from the raw maize.