Steering the EU food system towards a sustainability transformation requires a vast and actionable knowledge base available to a range of public and private actors. Few have captured this complexity by assessing food systems from a multi-dimensional and multi-level perspective, which would include (1) nutrition and diet, environmental and economic outcomes together with social equity dimensions and (2) system interactions across country, EU and global scales. This paper addresses this gap in food systems research and science communication by providing an integrated analytical approach and new ways to communicate this complexity outside science. Based on a transdisciplinary science approach with continuous stakeholder input, the EU Horizon2020 project ‘Metrics, Models and Foresight for European SUStainable Food And Nutrition Security’ (SUSFANS) developed a five-step process: Creating a participatory space; designing a conceptual framework of the EU food system; developing food system performance metrics; designing a modelling toolbox and developing a visualization tool. The Sustainable Food and Nutrition-Visualizer, designed to communicate complex policy change-impacts and trade-off questions, enables an informed debate about trade-offs associated with options for change among food system actors as well as in the policy making arena. The discussion highlights points for further research related to indicator development, reach of assessment models, participatory processes and obstacles in science communication.