A system and method for making an enhanced cheese product includes a milk processing system for developing cheese curd (124), and a mixing means (156) which mixes the cheese curd and the enhancing agent. By applying negative pressure to a mixture of cheese curd and enhancing agent, the enhancing agent can be drawn into the cheese curds. The enhancing agent may include whey protein to increase product. Likewise, probotics, fat substitute, enzymes and flavorings may be added to the cheese curds to produce cheese products with reduced spoilage, decreased fat, accelerated ripening or new flavors.