Mycotoxins are widespread natural toxins with diverse toxicological impacts, produced in crops like cereals in the field and/or post-harvest. Most common mycotoxins that occur at relatively high levels in maize are fumonisins, zearalenone, and aflatoxins. In addition, other mycotoxins such as deoxynivalenol are also frequently present in maize. Primary processing, such as cleaning and milling of grain can cause a redistribution of mycotoxins by fractionation. The current article comprehensively reviews the effect of cleaning, dry-milling, and wet-milling operations on mycotoxin concentrations in maize products. In doing so, industrial and traditional processing procedures were considered. Furthermore, the observed changes are set in relation to regulatory requirements in the European Union (EU) regarding mycotoxins in foodstuffs. In the EU, maximum levels are defined for unprocessed maize (uncleaned or cleaned), maize milling fractions intended for further processing, and final maize-based foodstuffs. The EU maximum levels address aflatoxins, ochratoxin A, fumonisins B-1 and B-2, zearalenone, and deoxynivalenol. Besides these regulated mycotoxins, the review also summarizes available data on other mycotoxins (e.g., nivalenol, T-2 toxin, and HT-2 toxin), including modified forms (i.e., hydrolysed fumonisin B-1 and acetyl-deoxynivalenol) and matrix-associated toxins (fumonisins). The effect of processing generally depends on several factors, which becomes particularly obvious in case of cleaning. During dry milling, the extent of reduction further relies, at least for Fusarium toxins, on the particle size. For flour, conformity with EU maximum levels may not always be given when applying good practices. Commercial wet milling shows a very high efficiency in lowering mycotoxin levels in starch.