The concept of the water–energy–food (WEF) nexus has become widely used to help understand interdependencies among the three systems, and how they can be managed sustainably to meet growing demand. The water–energy–food nexus has especially been advocated to address conflicts among the sectors. However, governance in the water–energy–food nexus has not received much attention in the literature, particularly the institutions and politics governing the water–energy–food sectors. This paper synthesises findings from CDKN-supported action research in this area. The paper draws from findings in Indonesia, Kenya and the Amazon Basin to show that the effectiveness of the horizontal (cross-sectoral) and vertical (between levels of government) coordination that is essential for a nexus approach is determined by institutional relationships, which can be influenced by political economy factors. The capacity of governing organisations to understand nexus links and to collaborate with each other is also critical. The paper suggests that aiming for the ideal of comprehensiveness and integration in a nexus approach may be costly and impractical. Nevertheless, horizontal and vertical coordination are essential. Local-level decision-making will determine how trade-offs and synergies in the water–energy–food nexus are implemented. The capacities of local government organisations and decision-makers need to be strengthened to enhance their capacity to adopt nexus approaches and coordinate vertically.