A single ecosystem dominates the Midwestern United States, occupying 26 million hectares in five states alone: the corn–soybean agroecosystem [Zea mays L.–Glycine max (L.) Merr.]. Nitrogen (N) fertilization could influence the soil carbon (C) balance in this system because the corn phase is fertilized in 97–100% of farms, at an average rate of 135 kg N·ha⁻¹·yr⁻¹. We evaluated the impacts on two major processes that determine the soil C balance, the rates of organic-carbon (OC) inputs and decay, at four levels of N fertilization, 0, 90, 180, and 270 kg/ha, in two long-term experimental sites in Mollisols in Iowa, USA. We compared the corn–soybean system with other experimental cropping systems fertilized with N in the corn phases only: continuous corn for grain; corn–corn-oats (Avena sativa L.)–alfalfa (Medicago sativa L.; corn–oats–alfalfa–alfalfa; and continuous soybean. In all systems, we estimated long-term OC inputs and decay rates over all phases of the rotations, based on long-term yield data, harvest indices (HI), and root : shoot data. For corn, we measured these two ratios in the four N treatments in a single year in each site; for other crops we used published ratios. Total OC inputs were calculated as aboveground plus belowground net primary production (NPP) minus harvested yield. For corn, measured total OC inputs increased with N fertilization (P < 0.05, both sites). Belowground NPP, comprising only 6–22% of total corn NPP, was not significantly influenced by N fertilization. When all phases of the crop rotations were evaluated over the long term, OC decay rates increased concomitantly with OC input rates in several systems. Increases in decay rates with N fertilization apparently offset gains in carbon inputs to the soil in such a way that soil C sequestration was virtually nil in 78% of the systems studied, despite up to 48 years of N additions. The quantity of belowground OC inputs was the best predictor of long-term soil C storage. This indicates that, in these systems, in comparison with increased N-fertilizer additions, selection of crops with high belowground NPP is a more effective management practice for increasing soil C sequestration.