Background Fine-tuning the aeration for cultivations when oxygen-limited conditions are demanded (such as the production of vaccines, isobutanol, 2–3 butanediol, acetone, and bioethanol) is still a challenge in the area of bioreactor automation and advanced control. In this work, an innovative control strategy based on metabolic fluxes was implemented and evaluated in a case study: micro-aerated ethanol fermentation. Results The experiments were carried out in fed-batch mode, using commercial Saccharomyces cerevisiae , defined medium, and glucose as carbon source. Simulations of a genome-scale metabolic model for Saccharomyces cerevisiae were used to identify the range of oxygen and substrate fluxes that would maximize ethanol fluxes. Oxygen supply and feed flow rate were manipulated to control oxygen and substrate fluxes, as well as the respiratory quotient (RQ). The performance of the controlled cultivation was compared to two other fermentation strategies: a conventional “Brazilian fuel-ethanol plant” fermentation and a strictly anaerobic fermentation (with ultra-pure nitrogen used as the inlet gas). The cultivation carried out under the proposed control strategy showed the best average volumetric ethanol productivity (7.0 g L −1 h −1 ), with a final ethanol concentration of 87 g L −1 and yield of 0.46 g ethanol g substrate −1 . The other fermentation strategies showed lower yields (close to 0.40 g ethanol g substrate −1 ) and ethanol productivity around 4.0 g L −1 h −1 . Conclusion The control system based on fluxes was successfully implemented. The proposed approach could also be adapted to control several bioprocesses that require restrict aeration.