This paper presents an in-depth exergy analysis of the ethanol fermentation process with various forms of fungus Mucor indicus under aerobic and anaerobic conditions to select the most productive and sustainable conditions. Various carbon sources including fructose, glucose, and sucrose as well as the whole and inverted sugar beet and sugarcanes molasses were used during the fermentation. The rational and process exergetic efficiencies were found to be in the range of 65.21%-88.54% and 0.00%-44.31%, respectively. Overall, the exergy-based parameter based on the process outputs could provide useful information about the sustainability and productivity of the fermentation process compared to the rational analysis. More specifically, the inverted sugar beet molasses with MF (mostly filamentous) form of M. indicus under anaerobic cultivation was shown to be the best option for industrial production phase with respect to the productivity and sustainability issues. The results obtained confirmed that the process yield alone cannot perfectly reflect the exact sustainability parameters of the renewable ethanol production systems. Finally, the developed exergetic framework could help engineers to couple biochemical and physical concepts more robustly for achieving the most cost-effective and eco-friendly pathways for bioethanol production. (C) 2016 Elsevier Ltd. All rights reserved.