Food systems must serve different societal, public health and individual nutrition, and environmental objectives and therefore face numerous challenges. Considering the integrated performances of food systems, this paper highlights five fundamental paradigm shifts that are required to overcome trade-offs and build synergies between health and nutrition, inclusive livelihoods, environmental sustainability and food system resilience. We focus on the challenges to raise policy ambitions, to harmonize production and consumption goals, to improve connectivity between them, to strengthen food system performance and to anchor the governance of food systems in inclusive policies and participatory institutions. Taken together, these shifts in paradigms shape a new discourse for food system transformation that will be capable to respond to current and future policy challenges.