This study presents an optimization model of the upstream supply chain of an oilseed based-biofuels production system. It has been developed considering West Africa rural context where family farming is mainly practiced. The model has been applied to a theoretical case of study on jatropha seeds supply chain. Four scenarios on farms surface area occupancy and on the transportation means used between farms and feedstock gathering points (GP) have been performed. Considering different farming systems, different seed yield, and different transportation mode, the results show that the most efficient option is the "intercropping" mode with the pre-processing operations located at the farms and with the transportation between farms and GP ensured by carts