Little information exists on the potential for N fertilizer application to corn (Zea mays L.) to affect N2O emissions during subsequent unfertilized crops in a rotation. To determine if N fertilizer application to corn affects N2O emissions during subsequent crops in rotation, we measured N2O emissions for 3 yr (2011–2013) in an Iowa, corn–soybean [Glycine max (L.) Merr.] rotation with three N fertilizer rates applied to corn (0 kg N ha−1, the recommended rate of 135 kg N ha−1, and a high rate of 225 kg N ha−1); soybean received no N fertilizer. We further investigated the potential for a winter cereal rye (Secale cereale L.) cover crop to interact with N fertilizer rate to affect N2O emissions from both crops. The cover crop did not consistently affect N2O emissions. Across all years and irrespective of cover crop, N fertilizer application above the recommended rate resulted in a 16% increase in mean N2O flux rate during the corn phase of the rotation. In 2 of the 3 yr, N fertilizer application to corn (0–225 kg N ha−1) did not affect mean N2O flux rates from the subsequent unfertilized soybean crop. However, in 1 yr after a drought, mean N2O flux rates from the soybean crops that received 135 and 225 kg N ha−1 N application in the corn year were 35 and 70% higher than those from the soybean crop that received no N application in the corn year. Our results are consistent with previous studies demonstrating that cover crop effects on N2O emissions are not easily generalizable. When N fertilizer affects N2O emissions during a subsequent unfertilized crop, it will be important to determine if total fertilizer-induced N2O emissions are altered or only spread across a greater period of time.