While the health impact of COVID-19 in most African countries appears modest, the impact of social distancing measures, closing of markets and reduced mobility is felt across the board. Domestic, labor-intensive and traditional food value chains and the smallholders they serve appear to be particularly affected. During a systemic shock where idiosyncratic risk coping strategies fail, collective or organizational resilience becomes of the essence to protect the livelihoods of smallholders. In this study, we have used pre- and during-shock data on agricultural cooperatives from Southeast Africa to understand how resilient these smallholder-owned organizations are. We find that many organizations could not countervail market-disruptions and fell into a state of dormancy during the pandemic. One reason for this is that collective decision-making was heavily affected by the banning of gatherings. Only a few organizations devised innovative solutions to maintain the market linkages of rural smallholders. The lack of resilience demonstrated by most cooperatives appears to be associated with organizational immaturity, large membership size, elite capture and limited business-orientation, which underscore a general lack of managerial capital.