Cheese ripening is usually described in terms of kinetics of proteolysis, lipolysis and aroma compound production, which provides an averaged view of ripening. However, after milk inoculation and rennet action, bacteria are immobilized as colonies into the curd and grow as such. This colonial distribution is a reality in all kind of cheeses. The efficiency of bacteria within these colonies to act on dairy matrices (gene expression and activity of the enzymes produced) will thus depend on local physico-chemical conditions, matrix structure, diffusion limitations and inter-colony distance. The ambition of our team is to understand the ripening mechanisms in situ at a microscopic scale level, considering the colonial distribution. For that purpose, the following fields were explored: i) to characterize the spatial distribution of bacterial colonies according to the level of inoculation by mathematical modelization and by in situ validation using confocal laser microscopy (Jeanson et al., 2011 Appl. Environ. Microbiol. doi:10.1128/AEM.02233-10); ii) to estimate the diffusion rate of small solutes in dairy matrices differing in composition and microstructure. Indeed diffusion of water and salt were extensively characterized (Floury et al., 2010 Dairy Sci. Technol. 90:477-508) but not the diffusion of small solutes which are crucial for the bacterial metabolic activity and the ripening reactions. Moreover, the impact of cheese composition and microstructure on this diffusion is far from being well understood. The diffusion coefficient of a small solute was estimated for the first time by a noninvasive way within a cheese matrix using new imaging approaches, the Fluorescence Recovery After Photobleaching and using fluorescent 4 and 20 kDa dextran molecules. iii) to reveal in situ bacterial enzymes within and around the colonies immobilised in cheese. Cell wall protease and intracellular peptidases were first detected in situ by immunofluorescent antibodies and confocal microscopy.