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 PGE, 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. The invention also provides soybean plants for use in producing seeds that have an overall improved bioactivity compared to other seeds as hydrolysates by combining effects on several bioactivity assays in a health index. The invention also provides products derived from, and parts of, these plants and uses thereof. Methods for producing such plants are also provided, as well as methods for standardizing or assuring quality control of soybean products with enhanced bioactivity for humans and animals.