Bacteria are immobilised in cheeses after the coagulation step whatever the technology. They grow as colonies and are the main agents of cheese ripening. However, questions remain at the microscopic scale about i) how metabolic activities of the bacterial colonies affect their surrounding micro-environment in the cheese matrix and (ii) the diffusion of solutes, such as potential substrates, from the cheese matrix into the colonies. The studies on immobilised bacterial colonies mainly deal with agar/gelatine media. The results demonstrate the major importance of the size and the distance between colonies, here called spatial distribution. We will first describe the spatial distribution of colonies in a model cheese as a function of the inoculation level. Then, on one side, we will show that the activities of bacteria, depending on the spatial distribution, influence or not, the micro-environment around the colonies, regarding pH and redox potential. On the other side, we will present the porosity of the colony to different examples of solutes of various properties (size, charge, shape...) able to diffuse, or not, inside the colony in a model cheese. Finally, we will discuss the potential consequences of different spatial distributions of colonies on the ripening process, by focusing on the metabolome of cheese or “cheesome