The anaerobic digestion process can represent a sustainable opportunity by converting organic waste products (OWP) into two economically useful by-products: a renewable energy source (biogas) and a potential fertilizer and soil amendment (anaerobic digestate). The use of anaerobic digestates as organic amendments could represent an alternative to conventional mineral fertilizers. However, it is imperative to rigorously assess their adverse or beneficial impacts in favor of environmental and soil protection. Their use at large scale in agricultural fields still requires in-depth investigations to draw objective and robust conclusions about the impact of digestates on soil biodiversity, especially their long-term effect on the soil microbial communities (Archaea, Bacteria and Fungi) which play an essential role in ecosystem functioning and resilience. The present work monitored, over a decade, the cumulative effect of repeated digestate application on soil microbial communities employing and in-situ approach, comparing the effect of the digested feedstock to the same undigested feedstock, and to others fertilization treatments. The study was carried out at the experimental field site EFELE, located in Rennes, France. The experiment was set up in 2012 and is based on a wheat-maize crop rotation. A mineral fertilizer (MIN), and three different OWP: cattle manure (CM), pig slurry (PS), and pig slurry anaerobic digestate (PS-DIG), were applied once every year since the beginning of the trial to the present. These treatments were compared to a control (0N) that had not received any organic or mineral N input. To monitor soil microbial community dynamics, from 2012 to 2022, soil samples were collected every year twelve months after the last fertilization treatment. For the molecular analyses performed in this study, soil samples belonging to the beginning of the trial (2012), and wheat crop years (2013, 2015, 2017, 2019, and 2022) were selected. Moreover in 2012, 2016, and 2021, from the same sampled soils, soil physicochemical analyses were performed. All the molecular analyses were conducted in 2022; we used high-throughput sequencing targeting 16S and 18S ribosomal RNA genes to describe the dynamics of microbial soil communities. From our results, it takes more than 5 years to detect a significant decrease of the Soil Organic Carbon (SOC) content after annual application of PS and PS-DIG. In contrast, in CM-treated plots, no significant changes in SOC content were noticeable over a decade. For all treatments except for 0N, the soil microbial biomass did not increase; instead, it remained stable, suggesting an equilibrium state after annual inputs. The composition and structure of soil microbial communities in all treatments were driven by the lasting modifications on soil physicochemical properties caused by the chemical composition of the product applied, and their lasting effects may take at least 5 years to become noticeable. Moreover, the temporal factor (year) had a strong influence, possibly highlighting environmental, climatic, and seasonal effects that could mask the impact of digestate on soil microorganisms. Further research is needed to better understand the cumulative effects of repeated digestate application on soil microbial communities, taking in count the agro-pedological context and the interaction with other agricultural practices.