In this work, a thermodynamic framework was proposed to achieve improved process understanding of ethanol and acetate fermentation in a continuous stirred tank bioreactor from syngas through the Wood–Ljungdahl pathway. The bioreactor performance was evaluated using both conventional exergy and eco-exergy principles to identify the effect of different operational parameters i.e. agitation speeds and liquid media flow rates as well as syngas volume flow rates and its composition on the sustainability and renewability of the process. The exergy efficiency of the bioreactor was found to be in the range of 8.14–89.51% and 8.86–89.52% using the conventional exergy and eco-exergy concepts, respectively. The maximum exergetic productivity index was found to be 6.82 and 6.90 using the conventional exergy and eco-exergy concepts, respectively, at agitation speed of 450rpm, liquid media flow rate of 0.55ml/min, and syngas volume flow rate of 8ml/min containing 10% CO2, 15% Ar, 20% H2, and 55% CO. In general, the exergetic performance parameters computed using both concepts under the studied conditions did not display significant differences because of the low volume of the bioreactor and slow growth rate of the microorganisms. The results of the present study showed that exergy concept and its extensions could undoubtedly play a strategic role in assessing biofuel production pathways with respect to the issues currently of major interest in the renewable energy industry, i.e., sustainability and productively.