Nitrous oxide (N₂O) emission from denitrification in agricultural soils often increases with N fertilizer and soil nitrate (NO₃) concentrations. Overwintering cover crops in cereal rotations can decrease soil NO₃ concentrations and may decrease N₂O emissions. However, mineralizable C availability can be a more important control on N₂O emission than NO₃ concentration in fertilized soils, and cover crop residue provides mineralizable C input. We measured the effect of a winter rye (Secale cereale L.) cover crop on soil N₂O emissions from a maize (Zea mays L.) cropping system treated with banded N fertilizer at three rates (0, 135, and 225 kg N ha^–1) in Iowa. In addition, we conducted laboratory incubations to determine if potential N₂O emissions were limited by mineralizable C or NO₃ at these N rates. The rye cover crop decreased soil NO₃ concentrations at all N rates. Although the cover crop decreased N₂O emissions when no N fertilizer was applied, it increased N₂O emissions at an N rate near the economic optimum. In laboratory incubations, N₂O emissions from soils from fertilizer bands did not increase with added NO₃, but did increase with added glucose. These results show that mineralizable C availability can control N₂O emissions, indicating that C from cover crop residue increased N₂O emissions from fertilizer band soils in the field. Mineralizable C availability should be considered in future evaluations of cover crop effects on N₂O emissions, especially as cover crops are evaluated as a strategy to mitigate agricultural greenhouse gas emissions.