A comprehensive assessment of policy impact on greenhouse gas (GHG) emissions from agricultural soils requires careful consideration of both socio-economic aspects and the environmental heterogeneity of the landscape. We developed a modelling framework that links the large-scale economic model for agriculture CAPRI (Common Agricultural Policy Regional Impact assessment) with the biogeochemistry model DNDC (DeNitrification DeComposition) to simulate GHG fluxes, carbon stock changes and the nitrogen budget of agricultural soils in Europe. The framework allows the ex-ante simulation of agricultural or agri-environmental policy impacts on a wide range of environmental problems such as climate change (GHG emissions), air pollution and groundwater pollution. Those environmental impacts can be analyzed in the context of economic and social indicators as calculated by the economic model. The methodology consists of four steps: (i) definition of appropriate calculation units that can be considered as homogeneous in terms of economic behaviour and environmental response; (ii) downscaling of regional agricultural statistics and farm management information from a CAPRI simulation run into the spatial calculation units; (iii) designing environmental model scenarios and model runs; and finally (iv) aggregating results for interpretation. We show the first results of the nitrogen budget in croplands in fourteen countries of the European Union and discuss possibilities to improve the detailed assessment of nitrogen and carbon fluxes from European arable soils.