In this study, the effects of microwave (MW) processing of germinated soybean seeds on moisture content and total polyphenol content (TPC) were studied. Germinated soybeans were processed at three different MW output powers (140, 280, and 420 W). By increasing the MW output powers (140–420 W), the drying time decreased from 15 to 6 min. The drying process took place in the falling rate period. Seven mathematical models for describing the thin-layer drying behavior of samples were investigated. The models were compared based on their R2, RMSE and x2 values between experimental and predicted moisture ratios. The results show that the Midilli model is the most appropriate model for drying behavior of thin layer samples. In addition, the kinetic study for the TPC degradation was conducted. According to the results, first-order kinetic models were fitted to experimental data. The activation energies of drying and TPC degradation process were 6.58 and 7.17 (W/g), respectively.