The optimal design and planning of glycerol-based biorefinery supply chains is critical for the development and implementation of this concept in a sustainable manner. To achieve this, a decision-making framework is proposed in this work, to holistically optimize the design and planning of the glycerol-based biorefinery supply chains under uncertainties. This framework presents a multilayered strategy composed of different steps, and it is strongly based on optimization techniques, detailed economic and environmental assessment, and multiobjective optimization under a stochastic environment. To maximize the business value, the economic objective is measured by the Net Present Value (NPV), whereas the environmental performance is measured by the estimation of a Single Indicator (SI) through the application of LCA methods. As part of the framework, a stochastic multiperiod, multiproduct, and multiechelon mixed integer linear programming problem is proposed based upon a previous model, GlyThink. In the new formulation, market uncertainties are taken into account at the strategic planning level. The robustness of the supply chain structures is analyzed based on statistical data provided by the implementation of the Monte Carlo method, where a deterministic optimization problem is solved for each scenario. Furthermore, the solution of the stochastic multiobjective optimization model points to the Pareto set of trade-off solutions obtained when maximizing the NPV and minimizing environmental consequences. Therefore, the proposed framework ultimately leads to the identification of the optimal design and planning decisions for the development of environmentally conscious biorefinery supply chains. The effectiveness of the presented approach is demonstrated through its application to the realistic case study of the glycerol-based biorefinery in Europe, where the results showed that the optimal solution under market uncertainties is obtained by establishing a multiplant supply chain for the glycerol-based integrated biorefinery, built upon two plant site locations (Germany, France) based on the production of succinic acid and lactic acid.