Four irrigated cropping systems of the Ecological Intensification experiment at the University of Nebraska, Lincoln, NE were compared regarding their potentials to emit N2O and CO2 from the soil surface. Greenhouse gas emissions were measured during the 2002 through 2004 growing seasons using gas chambers with photoacoustic infrared spectroscopy (PAS) detection. Daily emissions ranged from 0.23 to 116 g N2O-N ha-1 d-1 and 0.18 to 54.8 kg CO2-C ha-1 d-1 for recommended continuous maize (CCP1M1) and maize–soybean systems (CSP1M1) and 0.93 to 162.8 g N2O-N ha-1 d-1 and 1.03 to 52.3 kg CO2-C ha-1 d-1 for intensive cropping systems with increased plant population and nutrient input (CCP3M2 and CSP3M2). Seasonal N2O emission peaks were associated with high soil NO3 content, EC, soil/air temperature and water content. Average annual N2O emission in intensively managed continuous maize and maize following soybean was 7.5 kg N2O-N ha-1yr-1 as compared to 5.5 kg N2O-N ha-1 yr-1 in systems that followed recommended best management practices with lower nutrient inputs and yield targets (CCP1M1 and CSP1M1). However, in 2004, fine-tuned irrigation and crop management resulted in high yields and low N2O emissions with no differences among the four systems, indicating the potential for reduction of greenhouse gas emissions under intensive agriculture. Average annual CO2 emission estimates were 5.3 Mg CO2-C ha-1yr-1 for maize following soybean rotation and 6.8 Mg CO2-C ha-1yr-1 for continuous maize, suggesting that the CO2-emissions were significantly influenced by the amount and kind of crop residue returned to the field from the previous crop.