This article proposes a conceptual and methodological framework for analyzing agroecosystem resilience, in which aspects such as agrarian structure and peasant community agency are included as determining factors. The methodology is applied to a comparison of two peasant communities in Latin America (Brazil and Colombia), emphasizing the capacity to transform unsustainable power structures in place of adapting to them. We find that when agrarian structure is more equitable and peasant agency is strongly developed through political formation, organization and women's participation, then there is a greater construction of resilience that improves peasant livelihoods and dignity. This application demonstrates that when agency is strongly developed, as in the case of Brazil, it is possible to transform structural conditions that restrict resilience. The inclusion and consideration of biophysical variables, management practices, agrarian structure and agency, through a participatory approach, allows for the identification of factors that inhibit or potentiate the resilience of agroecosystems.