Anaerobic digestion of organic waste is considered 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 designed a microcosm experiment to compare the short-term (42-days) effects of four different digestates (derived from cattle manure, energy crop, food residues or slurry with bio-waste) on the soil microbial communities. Each digestate was applied on three contrasting soils representing a range of physicochemical characteristics (BOU, silty clay loam texture; PDL, loam texture and PACA, sandy loam texture). These soils are termed BOU, PDL and PACA hereafter, respectively. None of them had a historical record of digestate application; BOU and PDL were under annual cropping systems, while PACA was a vineyard soil. In addition, selected soils had never received digestates inputs before. Amended microcosms were compared to a control (undigested cattle manure). The effect of digestate inputs on the soil microbial communities was assessed using molecular DNA-based tools (quantification of extracted soil DNA and high-throughput sequencing) to measure microbial biomass and diversity, respectively. The impact of the digestates depended on the soil type. No digestate significantly affected the microbial biomass or diversity of the soil presenting the highest organic matter content (P > 0.05), as compared to the cattle manure. In the other soils, digestate addition led to lower microbial biomass compared to undigested manure. The intensity of this effect was dependent on the digestate type, and so were the microbial diversity indicators. Our results show that 42 days after biogas residue application, the effect of digestates on the soil microbial community structure depends on both the soil type and the digestate characteristics. To summarized, our results suggest that the soil microbial communities of coarse-textured soils with an acidic pH and a low C/N ratio are more sensitive to nitrogen-rich digestate inputs.