Presence of aflatoxins in agricultural products is a worldwide problem. Because of their high heat stability and resistance to most of the food processing technologies, aflatoxin degradation is still a big challenge. Thus, efficacy of pulsed electric fields (PEF) by energies ranging from 0.97 to 17.28 J was tested to determine changes in quality properties in red pepper flakes, mitigation of aflatoxins, inactivation of aflatoxin producing Aspergillus parasiticus, reduction in aflatoxin mutagenity, and modelling of A. parasiticus inactivation in addition to aflatoxin mitigation. Maximum inactivation rate of 64.37 % with 17.28 J was encountered on the mean initial A. parasiticus count. A 99.88, 99.47, 97.75, and 99.58 % reductions were obtained on the mean initial AfG1, AfG2, AfB1, and AfB2 concentrations. PEF treated samples by 0.97, 1.36, 5.76, and 17.28 J at 1 μg/plate, 0.97, 1.92, 7.78, 10.80 J at 10 μg/plate, and 0.97, 1.92, 2.92, 4.08, 5.76, 4.86, 6.80, 9.60, 10.80, and 10.89 J at 100 μg/plate were not mutagenic. Modelling with gradient boosting regression tree (GBRT), random forest regression (RFR), and artificial neural network (ANN) provided the lowest RMSE and highest R2 value for GBRT model for the predicted inactivation of A. parasiticus, whereas ANN model provided the lowest RMSE and highest R2 for predicted mitigation of AfG1, AfB1, and AfB2. PEF treatment possess a viable alternative for aflatoxin degradation with reduced mutagenity and without adverse effect on quality properties of red pepper flakes.