We propose a systematic framework for the selection of optimal processing pathways for a microalgaebased biorefinery under techno-economic uncertainty. The proposed framework promotes robust decision making by taking into account the uncertainties that arise due to inconsistencies among and shortage in the available technical information. A stochastic mixed integer nonlinear programming (sMINLP) problem is formulated for determining the optimal biorefinery configurations based on a superstructure model where parameter uncertainties are modeled and included as sampled scenarios. The solution to the sMINLP problem determines the processing technologies, material flows, and product portfolio that are optimal with respect to all the sampled scenarios. The developed framework is implemented and tested on a specific case study. The optimal processing pathways selected with and without the accounting of uncertainty are compared with respect to different objectives.