This article addresses redesigning the forest supply chain (FSC) to produce biomass-based fuels in synergy with existing fossil-based fuel production facilities under uncertainty. The decision-making problem simultaneously considers many aspects in which the forest supply chain must be adapted, including harvesting decisions, new processing facilities and technologies to efficiently produce alternative fuels from residual biomass obtained from multiple points of the supply chain, and changes in the demand for biofuels. The problem is formulated as a robust linear generalized disjunctive programming model that captures its logic and hierarchical nature while providing accurate and efficient results in terms of computational performance. A case study from the Argentinean Forest sector exemplifies the proposed approach.