In order for biobased industrial products to compete economically with petroleum-derived products, significant reduction in their processing cost is necessary. Since most bioprocesses are operated in batch or fed-batch mode, their optimization involves theoretical and computational challenges. Simulated annealing (SA), a stochastic optimization algorithm, is used in this study to solve a number of challenging optimization problems related to the design and operation of bioreactors. Two well-known case studies are considered in which the robustness and efficiency of the SA algorithm is demonstrated. More specifically, in the first case study it is shown that the global optimal solution located by SA achieves significant improved productivity when compared with the results of previous investigations. In the second case study a realistic objective function is considered where the economic performance of a bioprocess is optimized. SA exhibits impeccable performance and robustness and was able to locate the global optimal solution irrespective of the initial point selected.