Role of biobased fuel production takes a special role at international and European level. Microbial electrochemical systems (MEC– microbial electrolysis cell and MFC – microbial fuel cell) have a great energy production potential in combination with organic waste degradation. Energy efficiency of microbial systems and thus a positive effect to the greenhouse gas mitigation has been stated by many authors. However, due to the novelty of the technology and also availability of experimental MFC and MEC systems only, the environmental assessment of the microbial systems is not widely performed. This paper focuses on a comparative environmental analysis of MECs and MFCs based on life cycle inventory data.