This paper argues that supporting food system transformation requires more than obtaining science-based understanding and analysis of how components in the system interact. We argue that changing the emergent properties of food systems (what we call food system synthesis) is a socio-political challenge that is affected by competing views regarding system boundaries and purposes, and limited possibilities for central steering and control. We point to different traditions of ‘systems thinking’ that each emphasize particular types of interventions for achieving system change, and argue that food systems are best looked at as complex multi-dimensional systems. This implies that we need to move beyond rational engineering approaches to system change, and look for approaches that anticipate and accommodate inherent social tensions and struggles in processes of changing food system dynamics and outcomes. Through a case study on the persistence of an undesired emergent property of food systems (i.e. poverty) we demonstrate that a multi-level perspective (MLP) on system transformation is useful in understanding both how food system transformation has happened in the past, and how desirable transformations is prevented from happening today. Based on such insights we point to key governance strategies and principles that may be used to influence food system transformation as a non-linear and long-term process of competition, negotiation and reconfiguration. Such strategies include the creation and nurturing of diversity in the system, as well as process interventions aimed at visioning, destabilization and formation of discourse coalitions. Such governance interventions imply a considerable re-orientation of investments in food system transformation as well as a rethinking of the role that policy-makers may play in either altering or reproducing undesirable system outcomes.