Bioelectrochemical systems (BESs) are devices capable of converting organic waste fraction present in wastewaters into useful energy vectors such as electricity or hydrogen. In recent years a large amount of research has been done on these unique systems in order to improve their performance both in terms of waste treatment as well as electric current production. Already there are plans to upscale this technology to convince the end-users of its potential. However, there are not many studies available on the life cycle of these systems with the current state of the art. In this article a methodology has been proposed to perform the life cycle assessment (LCA) of the BESs and some recommendations have been given which may be useful in carrying out LCA of these systems. Not only the direct benefits in terms of energy saved in aerating the wastewater treatment plants, but also the resulting saving in cost and electric power produced should be factored as well. The results of LCA should show that with current knowledge and existing materials, how well the MFCs compares with the existing treatment methods such as anaerobic digestion. Further, given the amount of research going on in this field, it is expected that with cheaper materials and better microorganisms, the technology will breakthrough even soon.