A method for removing isoflavones from a soy-based beverage is disclosed. The method includes processing a soy base by subjecting ground or milled soy beans to one or more of sonic vibration and ultrahigh pressure homogenization. The soy base is separated, using centrifugation, into a lipid phase substantially free from isoflavones and a serum phase containing isoflavones. One or more isoflavones are separated from the serum phase. The serum phase is mixed with the lipid phase.
