A model was developed to calculate carbon fluxes from agricultural soils. The model includes the effects of crop (species, yield and rotation), climate (temperature, rainfall and evapotranspiration) and soil (carbon content and water retention capacity) on the carbon budget of agricultural land. The changes in quality of crop residues and organic material as a result of changes in CO2 concentration and changed management were not considered in this model. The model was parameterized for several arable crops and grassland. Data from agricultural, meteorological, soil, and land use databases were input to the model, and the model was used to evaluate the effects of different carbon dioxide mitigation measures on soil organic carbon in agricultural areas in Europe. Average carbon fluxes under the business as usual scenario in the 2008–2012 commitment period were estimated at 0.52 tC ha−1 y−1 in grassland and −0.84 tC ha−1 y−1 in arable land. Conversion of arable land to grassland yielded a flux of 1.44 tC ha−1 y−1. Farm management related activities aiming at carbon sequestration ranged from 0.15 tC ha−1 y−1 for the incorporating of straw to 1.50 tC ha−1 y−1 for the application of farmyard manure. Reduced tillage yields a positive flux of 0.25 tC ha−1 y−1. The indirect effect associated with climate was an order of magnitude lower. A temperature rise of 1 °C resulted in a −0.05 tC ha−1 y−1 change whereas the rising CO2 concentrations gave a 0.01 tC ha−1 y−1 change. Estimates are rendered on a 0.5 × 0.5° grid for the commitment period 2008–2012. The study reveals considerable regional differences in the effectiveness of carbon dioxide abatement measures, resulting from the interaction between crop, soil and climate. Besides, there are substantial differences between the spatial patterns of carbon fluxes that result from different measures.