A method for manufacturing a soy protein concentrate having a low non-digestible oligosaccharide and high isoflavone content. The soy protein may have high saponin content. The method includes the use of a membrane in an ultrafiltration process to separate non-digestible oligosaccharides from protein, while retaining isoflavones and saponins with protein. The soy protein concentrate with a low non-digestible oligosaccharide and high isoflavone and saponin content is useful as a milk substitute and in drink mixes as well as an ingredient in other nutrition and health products.