Hydrogen peroxide-based Fenton or Fenton-like reactions have been used extensively for the remediation of organic pollutants in the contaminated sites. However, the effects of H₂O₂ or Fenton reactions on soil properties and microbial communities are not fully understood. In this study, the effects of H₂O₂ and different Fenton reagents including H₂O₂, H₂O₂/V₂O₃ and H₂O₂/citrate chelated ferric on soil properties and microbial communities were studied. The results showed that H₂O₂ was decomposed quickly in soil accompanied with obvious degradation of soil organic matter (SOM), dramatic increase of soil ammonium nitrogen, and slight change of soil nitrate nitrogen. High-throughput sequencing was used to analyze microbial multi-samples and biome structure in soil, and it was found that H₂O₂ and Fenton reagents significantly reduced soil microbial diversity.