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” was held by the Southeast Asian Regional Center for Graduate Study and Research in Agriculture (SEARCA) and the Asian Farmers’ Association for Sustainable Rural Development (AFA) from 8–9 December 2021. The consultation was organized in collaboration with United Nations Educational, Scientific and Cultural Organization (UNESCO), International Cooperation Centre of Agricultural Research for Development (CIRAD), Group For Research and Technology Exchanges (GRET), and with technical assistance from FAO Regional Office for Asia and the Pacific (RAP). It 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 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. This publication compiles the proceedings of the two-day virtual regional consultation and marks an important milestone in initiating a stocktaking of existing initiatives and collaborations between ARIs, inter-government agencies and family farmers’ organizations in the region with a specific focus on agroecology and sustainable food systems.