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Cereals and soybeans are the main food sources for the majority of Chinese. This study evaluated the effects of four common cooking methods including steaming, boiling, frying, and milking on selenium (Se) content and speciation in seven selenium bio-fortified cereals and soybeans samples. The Se concentrations in the selected samples ranged from 0.91 to 110.8 mg/kg and selenomethionine (SeMet) was detected to be the main Se species. Total Se loss was less than 8.1% during the processes of cooking except milking, while 49.1% of the total Se was lost in milking soybean for soy milk due to high level of Se in residuals. It was estimated that about 13.5, 24.0, 3.1, and 46.9% of SeMet were lost during the processes of steaming, boiling, frying, and milking, respectively. Meanwhile, selenocystine (SeCys2) and methylselenocysteine (SeMeCys) were lost completely from the boiled cereals. Hence, steaming and frying were recommended to cook Se-biofortified cereals in order to minimize the loss of Se.