Abstract. The knowledge of the effects of climate change on agro-ecosystems is fundamental to identify local actions aimed to maintain productivity and reduce environmental issues. This study investigates the effects of climate perturbation on the European crop and grassland production systems, combining the finding from two biogeochemical models. Accurate and high-resolution management and pedoclimatic data has been employed. Results has been verified for the period 1978–2004 (historical period) and projected until 2099 with two divergent intensities IPPC’s climate projections, RCP4.5 and RCP8. We provided a detailed overview on productivity and the impacts on management (sowing dates, water demand, nitrogen use efficiency). Biogenic GHG budgets (N2O, CH4, CO2) were calculated, including an assessment of their sensitivity to the leading drivers, and the compilation of a net carbon budget over production systems. Results confirmed that a significant reduction of productivity is expected during 2050–2099, caused by the shortening of the length of the plant growing cycle associated to the rising temperatures. This effect was more pronounced for the more pessimistic climate scenario (-13 % for croplands and -7.7 % for grasslands) and for Mediterranean regions, confirming a regionally distributed impact of climate change. Non-CO2 GHG emissions were triggered by rising air temperatures and increased exponentially over the century, being often higher than the CO2 accumulation of the explored agro-ecosystems, which acted as potential C sinks. Emission factor for N2O was 1.82 ± 0.07 % during the historical period, rising up to 2.05 ± 0.11 % for both climate projections. The biomass removal (crop yield, residues exports, mowing and animal intake) converted croplands and grasslands into net C sources (236 ± 107 Tg CO2eq y-1 in the historical period), increasing of more than 20 % during the climate projections. Nonetheless, crop residues demonstrate to be an effective management strategy to overturn the C balance. Although with a marked latitudinal gradient, water demand will double over the next few decades in the European croplands, whereas the benefit in terms of yield will not contribute substantially to balance the C losses due to climate perturbation.