This contribution presents the development of a generic two-stage stochastic Mixed Integer Linear Programming (MILP) modelling framework to optimise the systematic design and planning of spatially explicit, multi-period, multi-echelon and multi-feedstock lignocellulosic biomass-to-biobased products supply chain networks in terms of financial profitability accounting for biomass yield uncertainty. A demonstrative European case study is addressed involving the potential Hungarian lignocellulose-based ethanol and power production. Results show the effectiveness of the proposed decision-making tool at providing a quantitative analysis regarding the economic performance of different design configurations and their effects in terms of investment decisions.