The conceptual process design of novel bioprocesses in biorefinery setups is an important task, which remains yet challenging due to several limitations. We propose a novel framework incorporating superstructure optimization and simulation-based optimization synergistically. In this context, several approaches for superstructure optimization based on different surrogate models can be deployed. By means of a case study, the framework is introduced and validated, and the different superstructure optimization approaches are benchmarked. The results indicate that even though surrogate-based optimization approaches alleviate the underlying computational issues, there remains a potential issue regarding their validation. The development of appropriate surrogate models, comprising the selection of surrogate type, sampling type, and size for training and cross-validation sets, are essential factors. Regarding this aspect, satisfactory validation metrics do not ensure a successful outcome from its embedded use in an optimization problem. Furthermore, the framework’s synergistic effects by sequentially performing superstructure optimization to determine candidate process topologies and simulation-based optimization to consolidate the process design under uncertainty offer an alternative and promising approach. These findings invite for a critical assessment of surrogate-based optimization approaches and point out the necessity of benchmarking to ensure consistency and quality of optimized solutions.