Agro-industrial residues mostly are untreated and underutilized and without appropriate disposal can cause environmental pollution and negative impact on human and animal health. These wastes can be used for bioenergy production, however they contain various potentially valuable compounds like proteins, sugars and minerals. Agro-industrial by-products were classified and screened according to suitability for microbial fermentation. Five products were selected for multi criteria analysis: three existing flows – biogas, bioethanol and biodiesel, with use as transportation fuel or heat and power, and two alternative flows – single-cell oil and singe-cell protein that can be used as animal feed or for human nutrition. Multi criteria analysis (TOPSIS) were analyzed by 11 indicators from economic, environmental and engineering selection. Results show that three best priorities for product production from agro-industrial wastes are single-cell oil, single-cell protein and biogas accordingly.