This study examines the potential of an integrated bio-commodity supply-production center. Previous research has demonstrated the financial viability of circular bio-economies through Mixed Integer Linear Programming (MILP) or simulation. However, these models 1) do not incorporate the necessary logistics operations for biomass collection and storage, 2) do not integrate and optimize those with the requirements of multi-products line lot sizes. A Geographic Information System (GIS) based model is proposed, integrating insertion and genetic algorithms with a hybrid (ABM-DES) simulation model. A case study in Greece's Fthiotida region, a hub for olive cultivation, investigates the production of pellets, olive cakes, and pomace oil from prunings and Two-Phase Olive Mill Waste (TPOMW). The findings suggest that the model allows for a more accurate estimation of impacts when considering the supply and production operations. In particular, it shows how the frequency and lot sizes of replenishment cycles, influenced by the varying numbers of mechanized harvesters employed, significantly impacts the fluctuation observed in the return on investments. Running the model, it is found that the optimized system with two harvesters can reach a breakeven point, within just 36 months, and corresponding emissions of about 622,041 kgCo2eq. This provides a benchmark for other olive industries to harness unexploited resources.