The present invention is directed to nutritionally superior cheese products and their methods of manufacture. More particularly, this invention is directed to the manufacture of nutritionally superior cheese products having at least two phases wherein at least one phase is cheese (e.g., process cheese, uncured natural cheese, cured natural cheese, and the like) and at least one phase is a second edible phase (e.g., a cheese different from the first phase, vegetables, meats, mixtures of vegetables and meats, fruit, nuts, and the like). The nutritionally superior cheese products of the present invention are prepared by co-extruding the two or more phases such that the use of adhesives or heat to bind the at least two phases is not required. Nutritional supplements (e.g., vitamins, calcium, minerals, and the like) can be incorporated into one or more of the at least two phases.