Chitosan has been used in agriculture as a soil ammendment and as a soil deodorizer in composting. However, the effects of chitosan on soil after application are not fully understood. In this study, we incubated bacteria in soil with and without chitosan addition. The physico-chemical properties of the soil and the biological properties by gene analysis were determined. The chitosan application increased the soil content of nitrate nitrogen throughout the incubation and promoted nitrification in the soil. DNA was recovered from the treated soil by pre-treatment with phosphate buffer, although chitosan is known to inhibit DNA extraction. The chitosan application significantly changed the bacterial community structure and increased the relative abundance of Streptomycetales, Sphingobacteriales, Xanthomonadales, Cytophagales, etc. Functional prediction analysis using PICRUSt2 suggests that ammonia was supplied to the soil by deamination of chitosan during chitosan metabolism.