Methods and systems are provided for the extraction of protein rich flour and fiber rich flour from brewer's spent grains (BSG). The extraction of protein from the BSG may include preparing the BSG by controlling the temperature in a hot grain storage system and in some cases dewatering the BSG to acceptable moisture content levels. In extracting the protein rich and fiber rich flour, the BSG is conveyed to a device that dries, mills, and fractionates the BSG into separated protein and fiber extract.