Fertilized soils in maize-soybean [Zea mays L.-Glycine max (L.) Merr.) systems can produce substantial quantities of N₂O, depending on management practices. Few studies have measured N₂O emissions from soybean following maize fertilized at varied N rates. We conducted a 2-year study of N₂O emissions from both phases of a maize-soybean rotation in central Iowa, USA. Treatments were use of winter rye cover crop (Secale cereale L.) after both crops and a range of fertilizer N rates (0 to 224 kg ha^-1). Precipitation differed greatly between the two years, slightly below and substantially below the long-term average in 2011 and 2012, respectively. In the first year, N fertilizer application increased N₂O emissions in maize. Cover crops were found to reduce soil nitrate (NO₃^-) concentration in the maize phase of the rotation. However, in the first year N₂O production was only reduced by the cover crop at 0 kg N ha^-1 and was greater with the cover crop at a 135 kg N ha^-1 in the maize. No differences between cover crop or N rate treatments were found in the soybean phase of the rotation in the first year. These results suggest that the role of cover crops in immobilizing soil NO₃^- does not necessarily decrease N₂O emissions and that the effect of N fertilizer on N₂O production in the maize year may not extend to the following soybean year.