Mycotoxins are widely present from cereal crops to food products, posing a significant risk to food safety and causing serious health and economic losses. Therefore, it is imperative to develop a sustainable and efficient detoxification strategy to address mycotoxin contamination. Herein, a dye-decolorizing peroxidase, BaDyP, from the white-rot fungus Bjerkandera adusta was successfully expressed as a soluble form in Escherichia coli with the help of molecular chaperones. Purified recombinant BaDyP could efficiently degrade multiple mycotoxins including aflatoxin B1, zearalenone, and deoxynivalenol in the presence of mediators such as Mn2+ or 1-HBT. Meanwhile, their degradation products were identified using UPLC-MS/MS, including AFB1-diol, AFQ1, 15-OH-ZEN, HZEN, and C15H18O8. Furthermore, cell survival tests exhibited a significant reduction in the biological toxicity of these degradation products. These findings indicate that the use of dye-decolorizing peroxidase could be a promising approach for the effective removal of multiple mycotoxins in cereal crops and food products.