The consumption of food contaminated with aflatoxins causes severe harmful health effects, which can lead to death, in both humans and livestock. Therefore, the degradation of aflatoxins, particularly by biological methods, is considered a feasible technology for remediation of aflatoxin-contaminated products. In vitro, aflatoxin B1, B2, G1, and G2 were degraded by 25 U/mL of lipase with reduction percentages of 57.5, 71.7, 80.1, and 83.8%. This reduction increased to 81.3, 82.8, 86.9, and 90.7% via 200 U/mL of lipase, respectively. Protease was less effective than lipase in the degradation of aflatoxin B1, B2, G1, and G2 with reduction levels of 35.8, 54.9, 66.5, and 70.2%, respectively, at 25 U/mL of protease. This investigation offers new concepts for the quick screening of aflatoxin-degrading enzymes and offers a theoretical basis for the degradation of aflatoxins. Interactions between aflatoxin B1 (considered as a ligand) and proteins that were taken as receptors (Structure of Lipase PDB ID: 1DT3 and Protease PDB ID: 2PRO) were elucidated. The molecular modeling results of utilized compound showed a notable binding score and best Root Mean Square (RMS) define value, indicating efficient binding mode and appropriate interactions with amino acids of selected proteins.