Different mixtures of olive pomace (OP), olive mill wastewater (OMWW) and olive pruning residues (OPR) were aerobically co-composted under natural conditions. Compost temperature showed a sharp increase in the first 40 -60 days, followed by a stabilization at 60°C and a decline after 150 days, whereas compost water content ranged from 50% -55% to 25% -30%. Total and selective microbial counts were followed throughout the experiment by means of innovative (IMT) and conventional (CMT) microbiological techniques. Pseudomonas spp., anaerobic bacteria, actinomycetes, and fungi reached levels of 8, 7, 5 and 6 log CFU g -1 compost, respectively, with a slight depression after 30-80 days. Total and fecal coliforms strongly decreased during the composting process. The use of IMT allowed to detect a higher and more stable growth of microorganisms if compared to CMT. IMT was demonstrated to be an appropriate and reliable method for monitoring the microbial pools during the co-composting process.