Anaerobic digestion of organic waste is considered as a key process to produce renewable energy to meet the growing sustainable energy demand. The residues of this anaerobic digestion, called digestates, can be used in agriculture as soil amendments and improve crop yields. However, the effect of digestates on soil biota, especially on microorganisms is still debated and needs to be better documented before their use at large scale in agricultural fields. The objective of the present thesis was to assess the effect of digestates on soil microbial community in different geographical and pedoclimatic contexts on the French territory. This thesis is divided in two parts. The first part takes place in field experiments (SOERE-PRO (EFELE and PROspective) and DIGE’O (Obernai), where different types of digestate are applied since many years. The second part needs the construction of a network of 80 farms over 4 regions: Pays de la Loire, Bretagne, Bourgogne Franche-Comté, and Provence-Alpes-Côte d’Azur. These farms applied digestates since at least three years. For these two parts of the project, the abundance and diversity of soil microbial communities will be characterized by environmental metagenomic tools based on soil DNA extraction (Dequiedt et al., 2011). Microbial molecular biomass will be assessed by the estimation of the amount of extracted DNA. Bacterial and fungal community density will be evaluated by the quantification of the number of copies of 16S and 18S ribosomal genes by real-time PCR. Finally, the taxonomic diversity of bacteria and fungi will be characterized by high throughput sequencing (illumina) of 16S and 18S ribosomal genes. Altogether, this study will generate some scientific knowledge needed to objectively assess the implications of digestate applications for agricultural soil biodiversity.