With increasing livestock products, management of livestock slurry is becoming crucial. One of the solutions for it is the installation of biogas plants, which produce biogas and digestate. It is necessary for farmers to use digestate as fertilizer to sustainably generate the energy using this system. However, the impacts of the digestate on soil microbes was unclear. Here, we performed a pot trial with potato crops in each pot treated with five treatments (control, chemical fertilizer, wood-chip manure, wheat-straw manure and digestate) to compare each other responses. The 16S rRNA bacterial community structures were investigated at various stages of the potato growth. This study revealed that application of wood-chip manure and wheat-straw manure significantly increased phylum of Actinobacteria, Bacteroidetes, respectively, but application of digestate did not increase any phylum compared to other treatments four weeks after planting potatoes, which means that wood-chip manure and wheat-straw manure have much impact on soil microbial community than digestate. Further, these changed soil microbial community did not cause increase of pathogen in soil, so we can conclude that not only soil microbial community but also soil chemical property can be a factor for onset of potato disease such as potato scab.