The present invention provides an economical method to produce an improved soy protein concentrate from soybeans which have been genetically-modified to reduce or eliminate the raffinose, stachyose and lipoxygenase content and associated off-flavors. The improved soy protein concentrate is highly functional, has good palatability and high retention of vitamins, minerals and isoflavones, little or no indigestible oligosaccharides, and is low in fiber such that it can be used in place of soy protein isolates in many applications. Further, the low processing costs of the present invention result in an economical product which offers a superior alternative for lower value uses such as aquaculture diets, pet foods, calf milk replacers, and so forth.