AbstractMaintaining soil productivity and sustainability remains a challenge in the face of a changing global agricultural framework, which includes the primary threat of soil degradation in many regions. Although soil erosion contributes to land degradation, how reductions in fertiliser nitrogen (N) affect erosion and soil microbial communities in sloped farmland remains unclear. In this study, effects of reductions in fertiliser N from 300 kg ha−1 (N1) to 225 kg ha−1 (N2), 150 kg ha−1 (N3), and 75 kg ha−1 (N4) on runoff, sediment yield and microbial community structure were evaluated in 12 maize farmlands with a 10° slope in Southwest China. Soil chemical properties were analyzed, and bacterial 16S rRNA and fungal ITS1 were sequenced from extracted DNA. Runoff and sediment yield in maize were significantly lower in N1 and N2 than in N3 and N4 (p < 0.05). The microbial diversity was higher in N1 and N2 than in N3 and N4. The severe erosion associated with reductions in N input resulted in significant decreases in abundances of the bacterial phyla Proteobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Firmicutes, and Nitrospirae and fungal phyla Basidiomycota, Mortierellomycota, and Olpidiomycota. By contrast, abundances of the phyla Acidobacteria (bacteria) and Ascomycota and Glomeromycota (fungi) increased significantly with severe erosion. Distance‐based redundancy analysis indicated that cation exchange capacity, organic matter, and nitrate strongly influenced structure of bacterial and fungal communities. Reductions >25% in N fertiliser (N3 and N4) did not meet crop N requirements, and because of the reduction in surface coverage, soil erosion was exacerbated, and soil fertility and diversity and complexity of microbial communities decreased. The results elucidated effects of N input on soil erosion and soil microbiomes in a sloped agroecosystem with the aim to rehabilitate or restore degraded land and increase sustainable agriculture development.