This study aimed to evaluate the effect of physical treatments (ultrasound, microwave, ultraviolet light, and magnetic fields) on the activities of peroxidases from rice bran and soybean meal to degrade aflatoxins B1 and M1 in milk. The effects of physical treatments on peroxidase activities were evaluated. Peroxidases (0.015 U mL−1) were added to milk contaminated with aflatoxins B1 and M1 (5 ng mL−1) under refrigeration (4 °C, 24 h), and residual concentrations of mycotoxins were quantified. Physical treatments increased peroxidase activities from rice bran and soybean meal extracts. The most efficient treatment was ultraviolet light (365 nm, 45 min) applied to peroxidases extracted from rice bran; degradation increased by 16.7% and 10.6%, reaching 78.2% and 71.2% aflatoxins B1 and M1 in milk, respectively. Therefore, using low-cost peroxidase physically treated by ultraviolet light can be an alternative for the food indstry to mitigate aflatoxins B1 and M1 in milk.