A method for preparing cheeses, preferably natural cheeses, containing significant levels of soy protein is provided. The process uses enzymes (preferably proteinase) to treat the soy ingredients and to form soy protein hydrolyzates. The enzyme-treated soy ingredients are complexable with casein micelles. After a heat treatment step to deactivate the enzymes, the soy protein hydrolyzate is added to a milk substrate which is then clotted, preferably using conventional rennet, to form curds and whey. After separating the curds and whey, the curd is converted to cheese using conventional cheese-making procedures. Without the initial enzyme treatment, the intact soy ingredients would interfere with milk clotting, thereby preventing the formation of a normal cheese curd. The partially hydrolyzated soy protein used in the present invention does not significantly interfere with milk clotting mechanisms. Cheeses containing up to about 30 percent soy ingredients can be obtained.