The governance of food markets is a crucial element for efficiency and distributional effects. In this paper, we use a conceptual model to show that this governance itself is endogenous in an environment of weak contract enforcement and imperfect markets, and importantly depends on the value in the chain. We relate the predictions of the theory to empirical evidence on differences in supply chain governance in Africa across different commodity types. In doing so we offer an explanation as why private sector governance systems with interlinked market transactions have emerged for higher value crops but not for staple food crops. We discuss the efficiency and equity effects and the implications for policy.