Selenium (Se) is an essential micronutrient for humans and animals. Soybean (Glycine max L.) has played an integral part in Asian foods for many centuries, and more recently, it has been integrated into Western diets (Lu et al. 2018). Compared to inorganic Se, organic Se is safer and more effective for absorption by the human body. Typically, more than 80% of the Se in crop kernels are organic (Eiche et al. 2015), and organic Se mainly exists in protein (Wang et al. 2013, Deng et al. 2017). Soybean protein content is relatively high, which accounts for roughly 40% of the dry weight of seeds (Hu et al. 2014). Soybean is widely planted and used for processing in China. They are harvested and processed into a variety of soybean products for human consumption. After a series of treatments and processing, Se concentration is bound to change. How Se is distributed in various Se-enriched soybean products is the primary concern in the development and utilization of Se-enriched soybean.