Impacts of reactive nitrogen (N) inputs on ecosystem carbon (C) dynamics are highly variable, and the underlying mechanisms remain unclear. Here, we proposed a new conceptual framework that integrates plant, microbial, and geochemical mechanisms to reconcile diverse and contrasting impacts of N on soil C. This framework was tested using long-term N enrichment and acid addition experiments in a Mongolian steppe grassland. Distinct mechanisms could explain effects of N on particulate and mineral-associated soil C pools, potentially explaining discrepancies among previous N addition studies. While plant production predominated particulate C changes, N-induced soil acidification strongly affected mineral-associated C through decreased microbial growth and pH-sensitive associations between iron and aluminum minerals and C. Our findings suggest that effects of N-induced acidification on microbial respiration and geochemical properties should be included in Earth system models that predict ecosystem C budgets under future N deposition/input scenarios.