The co-composting of olive oil mill wastes and household refuse was followed for 5 months. During the thermophilic phase of composting, the aerobic heterotrophic bacteria (AHB) count, showed a significant rise with a slight regression of fungal biomass. In the same way, phospholipid fatty acids PLFAs common in bacteria, showed a significant increase of hydroxyl and branched PLFAs. The evaluation of the ratio of octadecenoic PLFAs to stearic acid (C18:1omega/C18:0) revealed a significant reduction while a significant rise in the length of aliphatic chains evaluated by the stearic acid to palmitic acid ratio (C18:0/C16:0) was noted during the stabilization phase. The follow-up of PLFAs, indicates the degree of biodegradation that occurs during composting, it can be regarded an indicator of the stability and maturity of the end product.