In this work, mathematical modeling was employed to assess the dynamic behavior of the flash fermentation process for the production of butanol. This process consists of three interconnected units as follows: fermentor, cell retention system (tangential microfiltration), and vacuum flash vessel (responsible for the continuous recovery of butanol from the broth). Based on the study of the dynamics of the process, suitable feedback control strategies [single input/single output (SISO) and multiple input/multiple output (MIMO)] were elaborated to deal with disturbances related to the process. The regulatory control consisted of keeping sugar and/or butanol concentrations in the fermentor constant in the face of disturbances in the feed substrate concentration. Another objective was the maintenance of the proper operation of the flash tank (maintenance of the thermodynamic equilibrium of the liquid and vapor phases) considering that oscillations in the temperature in the tank are expected. The servo control consisted of changes in concentration set points. The performance of an advanced controller, the dynamic matrix control, and the classical proportional-integral controller was evaluated. Both controllers were able to regulate the operating conditions in order to accommodate the perturbations with the lowest possible alterations in the process outputs. However, the performance of the PI controller was superior because it showed quicker responses without oscillations.