Fed-batch fermentation is an important production technology in the biochemical industry. Using fed-batch Saccharomyces cerevisiae fermentation as a prototypical example, we developed a general methodology for nonlinear model predictive control of fed-batch bioreactors described by dynamic flux balance models. The control objective was to maximize ethanol production at a fixed final batch time by adjusting the glucose feeding rate and the aerobic-anaerobic switching time. Effectiveness of the closed-loop implementation was evaluated by comparing the relative performance of NMPC and the open-loop optimal controller. NMPC was able to compensate for structural errors in the intracellular model and parametric errors in the substrate uptake kinetics and cellular energetics by increasing ethanol production between 8.0% and 14.7% compared with the open-loop operating policy. Minimal degradation in NMPC performance was observed when the biomass, glucose, and ethanol concentration and liquid volume measurements were corrupted with Gaussian white noise. NMPC based on the dynamic flux balance model was shown to improve ethanol production compared to the same NMPC formulation based on a simpler unstructured model. To our knowledge, this study represents the first attempt to utilize a dynamic flux balance model within a nonlinear model-based control scheme. (C) 2016 Elsevier Ltd. All rights reserved.