Cover crops (CC) promote the accumulation of soil organic carbon (SOC), which provides multiple benefits to agro‐ecosystems. However, additional nitrogen (N) inputs into the soil could offset the CO2 mitigation potential due to increasing N2O emissions. Integrated management approaches use organic and synthetic fertilizers to maximize yields while minimizing impacts by crop sequencing adapted to local conditions. The goal of this work was to test whether integrated management, centered on CC adoption, has the potential to maximize SOC stocks without increasing the soil greenhouse gas (GHG) net flux and other agro‐environmental impacts such as nitrate leaching. To this purpose, we ran the DayCent bio‐geochemistry model on 8,554 soil sampling locations across the European Union. We found that soil N2O emissions could be limited with simple crop sequencing rules, such as switching from leguminous to grass CC when the GHG flux was positive (source). Additional reductions of synthetic fertilizers applications are possible through better accounting for N available in green manures and from mineralization of soil reservoirs while maintaining cash crop yields. Therefore, our results suggest that a CC integrated management approach can maximize the agro‐environmental performance of cropping systems while reducing environmental trade‐offs.