According to the invention a novel vegetable protein fractionation procedure is disclosed which includes a straightforward process to obtain 7S-rich (.beta.-conglycinin-rich) and 11S-rich (glycinin-rich) isolated protein fractions with unique functional and nutritional properties desired by the food industry. The process is much simplified compared to the art and avoids multiple steps in the usual fractionation of soy protein and uses very small amounts of salts avoiding the necessity of excessive washing and desalting steps. The process yields high amounts of protein fractions with high isoflavone contents and improved functional properties.