Soil microbial communities in wheat fields in East China respond differently to biochar and manure applications. High rates of biochar and manure increase bacterial richness by changing soil pH and reducing arsenic and copper levels. Biochar promotes certain bacterial classes, while manure inhibits others. Fungal communities also react to biochar and manure, with biochar restricting some classes and manure affecting others. These findings show that soil microbes are sensitive to changes in soil conditions caused by organic amendments, like biochar and manure, in agricultural systems.