Abstract: The invention provides a method that uses enzyme-treatment of whole soybeans or partially defatted soybeans to select soybeans with improved bioactivity or bioactivities. The invention further provides a soybean plant and seed with a non-transgenic mutation conferring enhanced bioactivity as an hydrolysate when compared to hydrolysate from other seeds, for instance in a cell-based assay, including reduced cancer cell viability; increased LDL receptor activity; reduced lipid accumulation; increased adiponectin expression; decreased FAS and LPL expression; reduced production of NO and PGE2, and expression of iNOS and COX-2; higher antioxidant activity; promotion of growth of bifidobacteria; and inhibiting the growth of pathogenic bacteria; for instance when compared to other seeds tested as hydrolysates.