The global food system faces significant vulnerabilities due to pandemics, which not only disrupt economies and governmental functions but also threaten food security and public health. Organic farming, particularly within cooperatives, plays a crucial role in promoting sustainable agriculture and enhancing rural development while contributing to ecosystem protection. This study investigates the production efficiency of 306 agricultural cooperatives in Hung Yen Province, Vietnam, before and during the COVID-19 pandemic. The efficiency assessment utilizes the analytic hierarchy process (AHP) model to examine the influence of factors such as the potential of cooperatives, labor resources, production processes, supply chains, and governmental support on the technical efficiency of these cooperatives. The findings indicate that organic cooperatives in Hung Yen maintained production efficiency throughout the pandemic, largely due to the adoption of advanced technologies and active participation in supply chains, which facilitated swift adaptation to new challenges. Among the influencing factors, the internal potential of cooperatives, labor resources, product development processes, and supply chain dynamics were identified as the most significant, whereas governmental support was found to have the least impact (0.07 for the first group, 0.06 for the second, and 0.06 for the third) during the pandemic. Additionally, three key factors—years of operational experience, product diversity, and business procedure support—were determined to have the greatest effect on production efficiency across different cooperative groups in the COVID-19 context. The study underscores the importance of enhancing the intrinsic potential of organic cooperatives to better adapt to rapid changes, thereby supporting rural development and agricultural productivity in the face of economic shocks such as the COVID-19 pandemic.