Fresh agricultural products (FAPs) require special handling to maintain product quality, especially during socio-economic crises. In developing countries, there is a compelling need for a robust supply chain governance strategy to regulate the supply chain actors involved in the logistics and distribution system. This paper proposes an innovative way to design FAP logistics governance to address specific problems in the FAP logistics networks of developing countries, where FAP supply chains are not well integrated. Three logistics governance scenarios were modelled using discrete-event simulation. The results revealed that the fully distributed governance could effectively reduce process delay and consequently minimise logistics costs, especially within the logistics networks serving multiple markets. This is due to that fact that the distributed governance allows the actors involved in the network to have some autonomy to manage their resources. The paper contributes to improving the fundamental understanding of the governance for FAP logistics networks consisting of small-holder farms. Our work also offers valuable insights for policymakers and practitioners into how to improve FAP supply chain management.