Farming practices that lead to declining returns and inputs of carbon (C) to soils pose a threat to soil functions by reducing availability of organic matter for soil microbes and by affecting soil structure, and soil C stocks that are key to regulating greenhouse gas emissions. SmartSOIL focuses on arable and mixed farming systems in Europe and will develop an innovative approach using the soil C flow and stocks concept to assess the impact of C management on crop productivity, soil organic C (SOC) stocks and other ecosystem services. SmartSOIL will identify and develop options to increase C stocks and optimise C use (flows) whilst maintaining sustainable SOC stocks. The flow and stocks concept will delineate short- versus long-term management effects on vital soil functions through meta-analyses of data from European long-term experiments (LTEs), as well as new measurements within LTEs. The new understanding will be used to improve existing soil and crop simulation models and test the models against independent LTE data. The models will then be used to derive a simplified model to estimate the short- and long-term effects of management on crop productivity and SOC storage. Scenarios of future management systems in Europe for improved productivity and enhanced SOC sequestration will be evaluated under current and future climate. The cost-effectiveness of alternative policy measures and options for managing SOC flows and stocks for improved productivity and SOC storage will be assessed based on the simplified model. SmartSOIL will develop a decision support tool (DST) to enable farmers, advisors and policy makers to discuss and select the most appropriate and cost-effective practices for particular farming systems, soils and climates. SmartSOIL will engage key stakeholders in case study regions and the wider EU in the development of the DST, guidelines and policy recommendations, and will inform the scientific and user community on progress and results.