Although policymakers and scientists are increasingly embracing the food system perspective, it has been poorly reflected in institutional terms. We aim to fill this gap by addressing the question as to what forms of governance are most appropriate to govern food systems in a more holistic way. The article presents a diagnostic framework consisting of five principles: 1) system-based problem framing to deal with interlinked issues, drivers and feedback loops; 2) connectivity across boundaries to span siloed governance structures and include non-state actors; 3) adaptability to flexibly respond to inherent uncertainties and volatility; 4) inclusiveness to facilitate support and legitimacy; and 5) transformative capacity to overcome path dependencies and create adequate conditions to foster structural change.