Cheese, a product of microbial fermentation may be defined as a protein matrix entrapping fat, moisture, minerals and solutes as well as dispersed bacterial colonies. The cheese matrix is an immensely complex and dynamic system, particularly during ripening. Knowledge gaps persist relating to the influence of manufacture parameters on structural and physicochemical characteristics of the matrix, on levels of inhomogeneity of these parameters within individual cheese blocks and in turn on their influence on the metabolic activity of entrapped bacteria. The advent of recent and more sophisticated analytical techniques, particularly in the fields of microstructure, microscopy and flow cytometry, now offers the opportunity to gain a deeper understanding of these factors during cheese ripening. This review considers levels of inhomogeneity of physico-chemical parameters such as pH observed at local level within cheese matrices and the influence of manufacture processes, including salting, on the in situ metabolic activity of starter bacteria within the cheese matrix. In addition it explores the influence of supplementation of curd with milk fat globule membrane material on subsequent cheese microstructure, ripening and sensory quality. Overall, a greater understanding of the influence of cheese manufacture parameters on microstructure and starter metabolic activity will facilitate the manufacture of cheeses with enhanced quality and consistency.