Due to the increasing demand of energy and environmental concern of fossil fuels, it is becoming increasingly important to find alternative renewable energy sources. Biofuels produced from lignocellulosic biomass feedstock's show enormous potential as a renewable resource. Electricity generated from the combustion of biomass is also one important type of bioenergy. Renewable resources like wind also show great potential as a resource for electricity generation. In order to deliver competitive renewable energy products to the end-market, robust renewable energy supply chains (RESCs) are essential. Research is needed in two distinct types of RESCs, namely: 1) lignocellulosic biomass-to-biofuel (LBSC); and 2) wind energy/biomass-to-electricity (WBBRESSC). LBSC is a complex system which consists of multiple uncertainties which include: 1) purchase price and availability of biomass feedstock; 2) sale price and demand of biofuels. To ensure LBSC sustainability, the following decisions need to be optimized: a) allocation of land for biomass cultivation; b) biorefinery sites selection; c) choice of biomass-to-biofuel conversion technology; and d) production capacity of biorefineries. The major uncertainty in a WBBRESC concerns wind speeds which impact the power output of wind farms. To ensure WBBRESC sustainability, the following decisions need to be optimized: a) site selection for installation of wind farms, biomass power plants (BMPPs), and grid stations; b) generation capacity of wind farms and BMPPs; and c) transmission capacity of power lines. The multiple uncertainties in RESCs if not jointly considered in the decision making process result in non-optimal (or even infeasible) solutions which generate lower profits, increased environmental pollution, and reduced social benefits. This research proposes a number of comprehensive mathematical models for the stochastic optimization of RESCs. The proposed large-scale stochastic mixed integer linear programming (SMILP) models are solved to optimality by using suitable decomposition methods (e.g. Bender's) and appropriate metaheuristic algorithms (e.g. Sample Average Approximation). Overall, the research outcomes will help to design robust RESCs focused towards sustainability in order to optimally utilize the renewable resources in the near future. The findings can be used by renewable energy producers to sustainably operate in an efficient (and cost effective) manner, boost the regional economy, and protect the environment.