Supply chains are complex interdependent structures in which tasks' accomplishment is the result of a compromise between all the entities involved. This complexity is particularly pronounced when dealing with chipping and transportation tasks within a forest-based biomass energy production supply chain. The logistic costs involved are significant and the number of network nodes are usually in a considerable number. For this reason, efficient optimization tools should be used in order to derive cost effective scheduling. In this work, soft computing optimization tools, namely genetic algorithms (GA) and particle swarm optimization (PSO), are integrated within a discrete event simulation model to define the vehicles operational schedule in a typical forest biomass supply chain. The presented simulation results show the proposed methodology effectiveness in dealing with the addressed systems.