This Special Issue of Sustainability aims at compiling original theoretical, methodological, and empirical research exploring how agroecology approaches can promote the transition towards sustainability, particularly of agri-food social-ecological systems, taking into account the complex relationships established between ecological functions and ecosystem services, human wellbeing, innovative socio-technical innovations, and governance models as well as public policies. In this editorial, we carry out an overview of the 17 contributions that shape this number, around five main themes: Agroecological practices that enhance ecosystem services, the potential of agroecology to promote social learning and innovation, gender and feminist perspectives in agroecology, the political articulation of agroecology, and public policies and the institutionalization of agroecology. Finally, we reflect about suggested guidelines for agroecology research that truly aims at supporting the transition towards strong social-ecological sustainability, we then deepen on the main gaps revealed by the research works presented. Finally, we conclude with the insights provided by agroecology within the transition towards social-ecological sustainability.