Cover crops and in-season nitrogen (N) management are promoted as key conservation practices for reducing nitrate leaching losses from agricultural fields. However, their combined effects on soil nitrous oxide (N2O) emissions per unit of crop productivity remains uncertain. These practices might contribute to high N2O emissions by providing N and C substrates for microbial denitrification activity, especially when in-season N application coincides with cover crop decomposition. The objective of this study was to evaluate the effects of N application timing and cereal rye (CR, Secale cereale L) cover crops on area- and yield-scaled soil N2O emissions in continuous maize (Zea mays L.) over 3-yr (2018–2020). Treatments were: Pre-Season-N: 224 kg N ha-1 split-applied in fall + pre-plant in 2018, or as single pre-plant applications in 2019 and 2020; In-Season-N: pre-plant + side-dress (growth stage V6-V7); In-Season-N + CR: ; and a zero N plot as the Control. We found that shifting from pre-season to in-season split N application did not significantly affect area- or yield-scaled N2O emissions in any year. Despite high N2O spikes for the In-Season-N + CR following side-dress N application in all years, this did not translate to consistently higher cumulative N2O emissions. Compared with Pre-Season-N and In-Season-N, In-Season-N + CR significantly increased area- and yield-scaled N2O emissions by approximately 50% in 1 of 3 years. These results suggest the combination of high soil N supply, warm and wet soil conditions, and cover crop decomposition contributes to elevated N2O emissions, but the cumulative effects of side-dress N application with a CR cover crop are variable across years. With increasing adoption of these practices to reduce nitrate leaching losses from croplands, future work should simultaneously assess effects on N2O emissions and crop yield to account for potential tradeoffs in N loss pathways.