Concerns about energy security and climate change have increased biofuel demand, particularly ethanol produced from cellulosic feedstocks (e.g., food crop residues). A central challenge to cropping for cellulosic ethanol is the potential environmental damage from increased fertilizer use. Previous analyses have assumed that cropping for carbohydrate in residue will require the same amount of fertilizer as cropping for grain. Using (13)C nuclear magnetic resonance, we show that increases in biomass in response to fertilization are not uniform across biochemical classes (carbohydrate, protein, lipid, lignin) or tissues (leaf and stem, grain, reproductive support). Although corn grain responds vigorously and nonlinearly, corn residue shows only modest increases in carbohydrate yields in response to high levels of fertilization (25% increase with 202 kg N ha(-1)). Lignin yields in the residue increased almost twice as much as carbohydrate yields in response to nitrogen, implying that residue feedstock quality declines as more fertilizer is applied. Fertilization also increases the decomposability of corn residue, implying that soil carbon sequestration becomes less efficient with increased fertilizer. Our results suggest that even when corn is grown for grain, benefits of fertilization decline rapidly after the ecosystem's N demands are met. Heavy application of fertilizer yields minimal grain benefits and almost no benefits in residue carbohydrates, while degrading the cellulosic ethanol feedstock quality and soil carbon sequestration capacity.