The present study describes the procedure followed to construct, to quantitatively validate and the utilization of a mathematical model to simulate ethanol production inside a large-scale bubble column bioreactor fed by syngas of two possible compositions i.e., pure CO and a 3:1 mixture of H2 and CO2. The model is structured by i) a black-box model for catabolic ethanol production and biomass growth and ii) a mass transfer model of the bioreactor; both parts are combined through hyperbolic uptake kinetics for CO and H2. Thermodynamics are used to study the production of energy through catabolism and to estimate biomass yields and maximum specific CO and H2 uptake rates. The simulation identifies a strong dependence of bioreactor performance and mass transfer rate of CO and H2. When mass transfer rate is above the 90 % of the maximum estimated values, ethanol productivity would reach 4.7 g/L/h, gas utilization would be 22 % and, the fermentation process plus the distillation of the product would require 7 MW/kg of ethanol produced. H2/CO2 fermentation achieved 20 and 30 % higher productivity and gas utilization than CO fermentation, respectively. Moreover, gas compression and distillation of ethanol are the largest contributors to energetic costs.