Bacteria are immobilized in cheese after the coagulation step whatever the technology. They grow as bacterial colonies and are the main agents of cheese ripening. However, questions remain, on the microscopic scale, about how metabolic activities of the bacterial colonies affect (i) the surrounding micro-environment of the cheese matrix and (ii) the diffusion of molecules from the cheese matrix into the bacterial colonies. Our objective was then developing non-destructive approaches, to be able to explore different parameters of the micro-environment around colonies and the porosity of colonies on the spatio-temporal scale. We used a model cheese inoculated with a Lactococcus strain and coagulated in an examination chamber. This setup allowed monitoring the changes of fluorescence intensity of dyes specific of pH and redox potential, using confocal microscopy. We also assessed the porosity of bacterial colonies by monitoring the diffusion of fluorescent molecules of different types and sizes (dextrans and proteins) inside colonies. As a result, we succeeded in measuring in situ the pH and the redox state around bacterial colonies, demonstrating, respectively, the absence and the presence of micro-gradients. This setup also allowed observing differences of diffusion behaviors, inside the colonies throughout time, depending on the type and the size of the diffusing molecules. These non-destructive approaches led to new insights about the interactions between the bacterial colonies and the cheese matrix, by describing changes in the micro-environment around bacterial colonies in a solid fermented food. It could now be adapted to more heterogeneous and complex cheeses, or any other fermented foods.