A food systems approach is critical to understanding and facilitating food system transformation, yet gaps in analysis are impeding changes towards greater equity, sustainability, and emancipation. Gaps include analyses of interdependencies among food system activities, of narrative politics, and of the behaviour of food system components using dynamic methodologies. Other problems include inappropriate boundaries to the system, insufficient learning across scales, lack of integration of social and ecological drivers and trends, and inadequate attention to the intersectional impacts of marginalisation. Both interdisciplinary and transdisciplinary work is necessary to overcome these problems, and, fundamentally, to understand power in food systems. Transdisciplinarity allows an engaged political economy in which social actors, including those who have not benefited from adequate food, livelihoods, and other services that food systems provide, are involved along with academics in co-creating the knowledge necessary for transformation. This engagement requires humility and respect, especially by academics, and explicit power-sharing.