The quality and commercial value of cheese are primarily determined by its physico-chemical properties (e.g., melt, stretch, flow, and color), specific sensory attributes (e.g., flavor, texture, and mouthfeel), usage characteristics (e.g., convenience), and nutritional properties (e.g., nutrient profile, bioavailability, and digestibility). Many of these functionalities are determined by cheese structure, requiring an appropriate understanding of the relationships between structure and functionality to design bespoke functionalities. This review provides an overview of a broad range of functional properties of cheese and how they are influenced by the structural organization of cheese components and their interactions, as well as how they are influenced by environmental factors (e.g., pH and temperature).