The multiple crises facing humanity at the onset of the Anthropocene are creating a moment in which agroecology acquires greater relevance as an alternative approach for meeting sustainable development goals and providing guidelines for the reconstruction of a post-COVID-19 agricultural system that is capable of minimizing future widespread disruptions of food supplies by pandemics and climate change by enhancing linkages between small-scale food production and local consumption. There are three main areas in which agroecology can be used in the development of a new post-COVID-19 agricultural system: revitalizing small farms, creating alternative animal production systems and enhancing urban agriculture. Focusing food and agricultural policies on agroecology as a main strategy for achieving autonomy and resilience can rapidly transform the ways in which we produce and consume food while addressing global challenges, including climate change, biodiversity loss, food insecurity, poverty, and deteriorating health.