Anaerobic digestion of organic wastes is considered as a key process to produce renewable energy to meet the growing sustainable energy demand. Digestates can be used in agriculture as soil amendments and improve crop yields. However, their use at large scale in agricultural fields still requires to prove their innocuity on soil biota, especially on microorganisms that play important roles in soil ecosystem. Here, we performed a microcosm experiment to compare the short-term effect (42-days) of 4 different digestates (derived from cattle manure, maize silage, food industry or slurry with bio-waste), each applied to 3 soils, on soil microbial communities. Soils were selected to represent a range of physicochemical and climatic characteristics and had never received digestates inputs. Amended microcosms were compared to a control (undigested cattle manure). The effect of inputs on soil microbial communities was assessed through molecular DNA-based tools allowing the measurement of microbial biomass (Soil DNA extraction / high throughput sequencing, respectively). The impact of digestates was soil type dependent. For soil microbial biomass and diversity, no digestates effect was observed for the soil presenting the highest organic matter content (P > 0.05). Concerning the other soils, in comparison with undigested manure, a decrease of microbial biomass was observed, but this was dependent on the nature of the digestate. A similar response was also observed on microbial diversity indicators. To conclude, our results suggest that 42 after biogas residues application, the effect of digestate on soil microbial communities depends on both soil type and the nature of the digestate.