Soil microorganisms are essential to maintain soil health and their functions depend on their community structures. They are influenced by agricultural practices, but the data obtained at the field level is limited. The study was conducted to determine effect of agricultural practices on soil microbial function and diversity in Kamishihoro, Hokkaido, Japan. Soils were sampled from where land use (cropland, grassland), season (summer, spring) and fertilizer history (biogas slurry, control) varied. Extracted soil DNA was sequenced for 16S bacterial gene with a next-generation sequencer. QIIME (bacterial community structure) and PiCRust (their functions) pipelines were used to assess the sequence data. For a few bacterial phyla, sampling site (rhizosphere and bulk soil), season and fertilizer had significant (p < 0.05) effect on their relative abundances (RA) in croplands. Fertilizer and season had a significant (p < 0.05) effect on RA of Acidobacteria, Chloriflexi among others in the grasslands. Fertilizer and season had significant (p < 0.05) differences on metabolites biosynthesis and membrane transport, respectively. Further investigation is needed to identify specific factors (such as soils’ chemical and physical changes) controlling the microbial community and its stability (against temperature/land use/farm management).