Climate-smart cropping systems should be designed with three objectives: reducing greenhouse gas (GHG) emissions, adapting to changing and fluctuating climate and environment, and securing food production sustainably. Agriculture can improve the net GHG emissions balance via three levers: less N2O, CH4 and CO2 emissions, more carbon storage, and green energy production (agrifuels, biogas). Reducing the application of mineral N fertilizer is the main option for reducing N2O emissions either directly or by increasing the proportion of legumes in the rotation. The most promising options for mitigating CH4 emissions in paddy fields are based on mid-season drainage or intermittent irrigation. The second option is storing more carbon in soil and biomass by promoting no-tillage (less fuel, crop residues), sowing cover crops, introducing or maintaining grasslands and promoting agroforestry. Breeding for varieties better adapted to thermal shocks and drought is mainly suggested as long-term adaptation to climate change. Short-term strategies have been identified from current practices to take advantage of more favorable growing conditions or to offset negative impacts: shifting sowing dates, changing species, cultivars and crop rotations, modifying soil management and fertilization, introducing or expanding irrigation. Some crops could also move to more suitable locations. Model-based tools and site-specific technologies should be developed to optimize, support and secure farmer's decisions in a context of uncertainty and hazards. Most of the adaptation and mitigation options are going in the same way but trade-offs will have to be addressed (e.g. increasing the part of legumes will be possible only with significant breeding efforts). This will be a challenge for designing cropping systems in a multifunctional perspective.