The Southeast Asian Regional Center for Graduate Study and Research in Agriculture (SEARCA) and the Asian Farmers’ Association for Sustainable Rural Development (AFA) jointly organized a two-day virtual regional consultation titled “Engaging with Academia and Research Institutions (ARIs) to Support Family Farmers and Food System Transformation During and Post COVID-19 Pandemic in Asia.” Held on 8–9 December 2021 via Zoom and Facebook Live, this was attended by 157 international participants and 51 speakers coming from different academic and research institutions (ARIs), non-governmental organizations (NGOs) and civil society organizations (CSOs), government agencies, and development partners. The consultation was organized in collaboration with the United Nations Educational, Scientific and Cultural Organization (UNESCO), Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), and Groupe de Recherches et d'Echanges Technologiques (GRET), with technical assistance from the Food and Agriculture Organization of the United Nations (FAO). The regional consultation highlighted the importance of collaboration among ARIs, family farmers’ organizations, government agencies, and development partners in Asia in enhancing the livelihoods of family farmers and developing their capacities to cope with the COVID-19 pandemic through Agroecology. Several recommendations emerged from the regional consultation, primarily on the transformation of agri-food systems. This transformation requires pragmatic thinking and farmer-led approaches, as well as inclusive partnerships and digital transition.