This study examines how meso-level institutions within Ostrom’s polycentric governance systems guide farmers’ deliberative preferences for collective adaptation to saltwater inundation in the Philippines and Viet Nam. Specifically, the paper investigates three mechanisms of meso-institutional influence: legitimacy creation, belief formation, and social enforcement that shape farmers’ collective adaptation. Using multinomial logistic regression with cluster-robust standard errors on survey data from rice farmers, results show that institutional embeddedness depends on both physical exposure and socioeconomic capacity; information access enhances belief accuracy and collective preferences in contexts where institutional trust is high; and legitimacy-based feasibility significantly strengthens support for collective measures. Findings also show country differences in managing high-externality adaptation measures, with only Viet Nam exhibiting sensitivity to institutional quality at higher externality levels. Comparative results reveal that autonomous, participatory meso-institutions in the Philippines generate stronger deliberative preferences and more cohesive collective adaptation than state-centred structures in Viet Nam.