A method is provided for producing an improved soybean product for use in food applications. The process enables the efficient denaturation of undesirable soy enzymes and removal of oligosaccharides from soybeans, preferably whole soybeans, without the development of off-flavors. The general method comprises: (1) heating an aqueous solution of a water soluble calcium salt to at least about 65 C. to provide a heated salt solution; (2) mixing soybeans with the heated salt solution to form a mixture; (3) heating the mixture for a time and at a temperature effective for deactivating protease inhibitors and lipoxygenase and removing oligosaccharides from the soybeans; (4) removing the aqueous solution from the mixture after the heating step; and (5) collecting the improved soybean product. The improved soybean product may be further processed for use in various food applications.