Estimation of the potential of new bioproducts is necessary to pre-design biorefineries with the highest relevance. A methodology assessing the relevance of such industrialized production involves is a multi-scale methodology describing a decision-support tool for the determination of an optimal biorefinery from a superstructure through process simulation, and economic and environmental evaluations. To optimize the biorefinery, energy integration was also applied on the selected processes, since a biorefinery needs a large amount of energy to operate, especially in the pretreatment and purification steps of the process due to huge water flowrate. Thus, the tool designs an efficient, profitable and sustainable biorefinery. The methodology capabilities were demonstrated with the acetone, butanol, and ethanol production from lignocellulosic biomass, especially from wood wastes.