Microbial communities in sewage sludge and green waste co-composting were investigated using culture-dependent methods and community level physiological profiles (CLPP) with Biolog Microplate. Different microbial groups characterized each stage of composting. Bacterial densities were high from beginning to end of composting, whereas actinomycete densities increased only after bio-oxidation phase i.e. after 40 days. Fungal populations become particularly high during the last stage of decomposition. Cluster analyses of metabolic profiles revealed a similar separation between two groups of composts at 67 days for bacteria and fungi. Principal component analysis (PCA) applied to bacterial and fungal CLPP data showed a chronological distribution of composts with two phases. The first one (before 67 days), where the composts were characterized by the rapid decomposition of non-humic biodegradable organic matter, was significantly correlated to the decrease of C, C/N, organic matter (OM), fulvic acid (FA), respiration, cellulase, protease, phenoloxidase, alkaline and acid phosphatases activities. The second phase corresponding to the formation of polycondensed humic-like substances was significantly correlated to humic acid (HA) content, pH and HA/FA. The influent substrates selected on both factorial maps showed that microbial communities could adapt their metabolic capacities to the particular environment. The first phase seems to be focused on easily degradable substrate utilization whereas the maturation phase appears as multiple metabolisms, which induce the release of metabolites and their polymerization leading to humification processes.