After its success in the treatment of wastewater sludges and agro-food industry effluents, the use of anaerobic digestion (AD) is now growing all over the world, being used to treat an increasingly wide range of wastes including livestock slurry, crops residues, green waste and urban waste. In this context, the stability of AD processes is a key issue for both biogas production and digestate quality, especially in installations mixing different types of wastes. The aim of this work was to study five full-scale digestion plants over the course of a year to analyse the influence of the type of substrate treated and type of process used on the digestate composition and microbial community structure in real working conditions. The studied plants were two agricultural, one centralized, and two urban digesters working under mesophilic and thermophilic conditions to treat both solid and liquid wastes. Sampling was conducted every 2 months. Digestate physico-chemical properties and microbiological compositions were studied using classical organic matter analyses (dry matter content, organic matter content, total carbon, total nitrogen, organic nitrogen, ammonia-nitrogen, and nitrous-nitrogen) and molecular microbiology techniques (16S rDNA-targeted quantitative PCR, molecular typing and Illumina MiSeq Next Generation Sequencing). The results show that overall the AD systems are remarkably stable except for the territorial AD process that was in its start-up phase: 1. The variation of the main characteristics of raw digestates was below 20% for 90% of the data, and below 10% for 50% of the data. The most important variation was obtained for the territorial plant. 2. Digestate composition is affected by the nature of the effluents and waste treated, particularly the nitrogen content, the ammonia/total nitrogen ratio and finally the carbon/nitrogen ratio of the raw digestate. Plants accepting manure produced digestate with ammonia/total nitrogen ratio above 60%. In contrast, digestate from municipal waste had higher C/N ratios due to lower initial nitrogen content. 3. The number of Bacteria remained stable in all plants at concentrations between 109 and 1010 gene copies/g of digestate except for the centralized AD process where the concentrations increased from 108 to 109 copies/g digestate. Again, this difference could be explained by the fact that this plant was still in start up procedure with an increasing loading rate. The number of Archaea methanogen represented between 5 and 20% of the total microorganisms and showed a similar stability at different plants as Bacteria (stability for all plants but the centralized AD which showed a 10 fold increase).