Nitrous oxide, carbon dioxide and methane are the main biogenic greenhouse gases (GHG) contributing to the global warming potential (GWP) of agro-ecosystems. Evaluating the impact of agriculture on climate thus requires a capacity to predict the net exchanges of these gases in an integrated manner, as related to environmental conditions and crop management. Here, we used two year-round data sets from two intensively-monitored cropping systems in northern France to test the ability of the biophysical crop model CERES-EGC to simulate GHG exchanges at the plot-scale. The experiments involved maize and rapeseed crops on a loam and rendzina soils, respectively. The model was subsequently extrapolated to predict CO2 and N2O fluxes over an entire crop rotation. Indirect emissions (IE) arising from the production of agricultural inputs and from cropping operations were also added to the final GWP. One experimental site (involving a wheat-maize-barley rotation on a loamy soil) was a net source of GHG with a GWP of 350 kg CO2-C eq ha 1 yr 1, of which 75% were due to IE and 25% to direct N2O emissions. The other site (involving an oilseed rape-wheat-barley rotation on a rendzina) was a net sink of GHG for –250 kg CO2-C eq ha 1 yr 1, mainly due to a higher predicted C sequestration potential and C return from crops. Such modelling approach makes it possible to test various agronomic management scenarios, in order to design productive agro-ecosystems with low global warming impact.