Knowledge of the effects of climate change on agro-ecosystems is fundamental to identifying 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 findings from two specific biogeochemical models. Accurate and high-resolution management and pedoclimatic data were employed. Results have been verified for the period 1978–2004 (historical period) and projected until 2099 with two divergent intensities: the Intergovernmental Panel on Climate Change (IPCC) climate projections, Representative Concentration Pathway (RCP) 4.5 and RCP8.5. We have provided a detailed overview of productivity and the impacts on management (sowing dates, water demand, nitrogen use efficiency). Biogenic greenhouse gas balance (N2O, CH4, CO2) was calculated, including an assessment of the gases' sensitivity to the leading drivers, and a net carbon budget on production systems was compiled. Results confirmed a rise in productivity in the first half of the century (+5 % for croplands at +0.2 t DM ha−1 yr−1, +1 % for grasslands at +0.1 t DM ha−1 yr−1; DM denotes dry matter), whereas a significant reduction in productivity is expected during the period 2050–2099, caused by the shortening of the length of the plant growing cycle associated with rising temperatures. This effect was more pronounced for the more pessimistic climate scenario (−6.1 % for croplands and −7.7 % for grasslands), for the Mediterranean regions and in central European latitudes, confirming a regionally distributed impact of climate change. Non-CO2 greenhouse gas emissions were triggered by rising air temperatures and increased exponentially over the century, often exceeding the CO2 accumulation of the explored agro-ecosystems, which acted as potential C sinks. The emission factor for N2O was 1.82 ± 0.07 % during the historical period and rose to 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 CO2 eq. yr−1 in the historical period), increasing from 19 % to 26 % during the climate projections, especially for RCP4.5. Nonetheless, crop residue restitution might represent a potential 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 (+2 % to +10 % over the century) will not contribute substantially to balance the C losses due to climate perturbation.