Indonesia is the sixth producer of cocoa beans in the world. Cocoa is one of the plantation commodities that plays an important role in Indonesia's economic development. A cocoa intermediary factory in middle Java Indonesia, is a producer of processed cocoa products and plays an important role in the distribution of cocoa beans in middle Java Indonesia. Transportation management of cocoa bean distribution from sub-district collectors to intermediary factories is not optimal. Because shipments from suppliers are uncertain, the number of transportation modes of transportation is not fixed, so that the allocation of transportation capacity is not fulfilled, distribution times are not appropriate, and long distances result in waste of transportation costs. This study proposes an agent-based simulation model for a complex cocoa distribution process. This simulation is then carried out several scenarios to get the optimization of the number of transportation modes and transportation costs.