Methods, compositions, and systems for steeping, propagation and fermentation, particularly large-scale operations for production of starch and ethanol and fermentation product streams are provided. Addition of mycotoxin mitigating enzymes or microorganisms expressing mycotoxin mitigating enzymes to steeping, propagation, and/or fermentation tanks, and/or to post-fermentation product streams, mitigates mycotoxin levels in fermentation co-products obtained from mycotoxin contaminated feedstocks.