Exergy is a thermodynamic quantity useful to obtain information on the work from any process. The analyses of irreversibility are important in the designing and development of the productive processes for the economic growth, but they play a fundamental role also in the analysis of socio-economic context. The link between the wasted exergy and the energy cost for maintain the productive processes are obtained in the bioengineering thermodynamics. This link holds to the fundamental role of fluxes and to the exergy exchanged in the interaction between the system and its environment. The equivalent wasted primary resource value is suggested as an indicator to support the economic considerations on the biofuel production by using biomass and bacteria. Moreover, the technological considerations can be developed by using the exergy inefficiency. Consequently, bacteria use can be compared with other way to obtain biofuels, by comparing both the technologies and the economic considerations.