In this study, the possibility to manage maize contaminated with aflatoxins and fumonisins for the production of biogas was considered. This is a priority in the climate change scenario that is expected to increase the occurrence of aflatoxins in maize. The results clearly underline how the anaerobic digestion process used in biogas plants is able to reduce aflatoxin contamination, mainly when highly contaminated maize is used for feeding the biodigestors without affecting the efficiency of methane production. In particular, the higher aflatoxin contamination is, the higher is mycotoxin reduction during biodigestion, with reductions up to 95% in digestate. The co-occurring mycotoxins, fumonisins, were also reduced by around 15%. The vitality of mycotoxin producing fungi was also significantly reduced. Biogas production is therefore suggested as a good alternative use for uncompliant maize.