In thermodynamics, the useful work in any process can be evaluated by using the exergy quantity. The analyses of irreversibility are fundamental in the engineering design and in the productive processes’ development in order to obtain the economic growth. Recently, the use has been improved also in the thermodynamic analysis of the socio-economic context. Consequently, the exergy lost is linked to the energy cost required to maintain the productive processes themselves. The fundamental role of the fluxes and the interaction between systems and their environment is highlighted. The equivalent wasted primary resource value for the work-hour is proposed as an indicator to support the economic considerations on the biofuel production by using biomass and bacteria. The equivalent wasted primary resource value for the work-hour is proposed as an indicator to support the economic considerations of 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 means of biofuel production, taking into account both the technologies and the economic considerations. Cyanobacteria results as the better organism for biofuel production.