Abstract: Methods are provided for making nutrient fortified foods, and particularly methods of fortifying cheeses and the resulting cheese products. These methods maximize nutrient retention in the final packaged product by fortifying desired portions of the food product and minimize fortification in other portions of the food product. Moreover the fortification methods described herein allow significant amounts of nutrient supplements to be delivered per serving of food product without adversely affecting functionality or product quality. Foods fortified by the disclosed methods retain their desired textures, mouthfeel, flavor, and other organoleptic properties.