Mycotoxins are naturally occurring fungal metabolites that are associated with health hazards and are widespread in cereals including maize. The most common mycotoxins in maize that occur at relatively high levels are fumonisins (FBs), zearalenone, and aflatoxins; furthermore, other mycotoxins such as deoxynivalenol and ochratoxin A are frequently present in maize. For these toxins, maximum levels are laid down in the European Union (EU) for maize raw materials and maize‐based foods. The current review article gives a comprehensive overview on the different mycotoxins (including mycotoxins not regulated by EU law) and their fate during secondary processing of maize, based on the data published in the scientific literature. Furthermore, potential compliance with the EU maximum levels is discussed where appropriate. In general, secondary processing can impact mycotoxins in various ways. Besides changes in mycotoxin levels due to fractionation, dilution, and/or concentration, mycotoxins can be affected in their chemical structure (causing degradation or modification) or be released from or bound to matrix components. In the current review, a special focus is set on the effect on mycotoxins caused by different heat treatments, namely, baking, roasting, frying, (pressure) cooking, and extrusion cooking. Production processes involving multiple heat treatments are exemplified with the cornflakes production. For that, potential compliance with FB maximum levels was assessed. Moreover, effects of fermentation of maize matrices and production of maize germ oil are covered by this review.