Bioethanol is one of the main liquid biofuels currently used. Usually the available sugar fractions are fermented anaerobically, which compromises the final yield of the product of interest. The present work had as objective to increase ethanol yield and productivity by using a control strategy based on metabolic fluxes that maintains microaerobic conditions in the bioreactor. The control logic was implemented in the SUPERSYS_HCDC program using the LabView 8.0 platform. Two validation cultures, about 12 h each, were performed in fed batch mode into a 5 L bioreactor using commercial S. cerevisiae (Baker´s yeast) and glucose as carbon source in minimal medium. Ethanol yield was 0.48 gethanol. gsubstrate-1 for both cultivations submitted to the metabolic fluxes control, which is very close to the theoretical maximum yield (0.51 gethanol. gsubstrate-1). The closed-loop control strategy favored low cells yields (0.10 gcells. gsubstrate-1) and low glycerol yields (0.076 gglycerol. gsubstrate-1). The proposed control strategy can be extended to other processes favored by microaerobic conditions.