Crop intensification is often thought to increase greenhouse gas (GHG) emissions, but studies in which crop management is optimized to exploit crop yield potential are rare. We conducted a field study in eastern Nebraska, USA to quantify GHG emissions, changes in soil organic carbon (SOC) and the net global warming potential (GWP) in four irrigated systems: continuous maize with recommended best management practices (CC-rec) or intensive management (CC-int) and maize–soybean rotation with recommended (CS-rec) or intensive management (CS-int). Grain yields of maize and soybean were generally within 80–100% of the estimated site yield potential. Large soil surface carbon dioxide (CO2) fluxes were mostly associated with rapid crop growth, high temperature and high soil water content. Within each crop rotation, soil CO2 efflux under intensive management was not consistently higher than with recommended management. Owing to differences in residue inputs, SOC increased in the two continuous maize systems, but decreased in CS-rec or remained unchanged in CS-int. N2O emission peaks were mainly associated with high temperature and high soil water content resulting from rainfall or irrigation events, but less clearly related to soil NO3-N levels. N2O fluxes in intensively managed systems were only occasionally greater than those measured in the CC-rec and CS-rec systems. Fertilizer-induced N2O emissions ranged from 1.9% to 3.5% in 2003, from 0.8% to 1.5% in 2004 and from 0.4% to 0.5% in 2005, with no consistent differences among the four systems. All four cropping systems where net sources of GHG. However, due to increased soil C sequestration continuous maize systems had lower GWP than maize–soybean systems and intensive management did not cause a significant increase in GWP. Converting maize grain to ethanol in the two continuous maize systems resulted in a net reduction in life cycle GHG emissions of maize ethanol relative to petrol-based gasoline by 33–38%. Our study provided evidence that net GHG emissions from agricultural systems can be kept low when management is optimized toward better exploitation of the yield potential. Major components for this included (i) choosing the right combination of adopted varieties, planting date and plant population to maximize crop biomass productivity, (ii) tactical water and nitrogen (N) management decisions that contributed to high N use efficiency and avoided extreme N2O emissions, and (iii) a deep tillage and residue management approach that favored the build-up of soil organic matter from large amounts of crop residues returned.