Biohemical processes and so-called hybrid biochemical processes, carried out in integrated unit operations such as membrane bioreactors, have found numerous applications in food and pharmaceutical process industries. However, such processes have hardly been investigated comprehensively. Dynamic modeling and especially dynamic optimization attempts were restricted because these unit operations combine continuous and discrete dynamic behavior and contain time and state events. In this paper we present a robust model of a process of high industrial significance, namely citric acid production in a membrane bioreactor, as well as a successful application of control parameterization numerical optimal control techniques to the fed-batch bioreactor and a membrane bioreactor. In order to evaluate the advantages and disadvantages of the design alternatives, the incremental objective function between batch and fed-batch, batch and different operations in a membrane bioreactor was formulated in terms of profit maximization. The determination of the optimal performance for the fed-batch fermenter and membrane bioreactor requires the solution of multiple optimal control problems, namely determining optimal feed and inlet concentration profiles, initial conditions and a production time. We show how the systematic combination of rigorous mathematical modeling: the integration of design and operational decisions and innovative discrete-continuous dynamic optimization techniques allow the generation of optimal designs and operating policies for hybrid biochemical processes that increase the profit of important production processes such as citric acid production.