Agriculture is the principal source for satisfying the growing global demand for food. However, current production patterns and socioeconomic and demographic pressures could lead to an unsustainable, inequitable food supply. Government interventions support technical advances designed to meet future needs following international trends while overcoming biophysical constraints. Those most often used are focused on augmenting land productivity through mechanisation and increased dependence on external inputs. To that end, public policies have emerged as engines of development in agriculture and the agri-food system. This article provides a chronological analysis of the relevant milestones in the agri-food sector in Ecuador (1960–2020). At first, agrarian reform focused on land distribution and tenure. Subsequently, the focus moved to the implementation of research, technological innovation and technology transfer programmes promoted by the state with support and financing from international organisations. For this article, we chose for our approach the water–energy–food nexus. Until now, insufficient study based on this approach regarding agricultural programmes has been conducted in Ecuador. It is essential to concentrate on this sector because it represents about 10% of the gross domestic product and is a principal source of employment for more than two-thirds of the economically active population in rural areas. However, land fractioning, the lack of project continuity and the focus on the application of technological packages identified in this analysis suggest the need to rethink public policies for a sustainable agri-food system.