Assuring environmental sustainable bioenergy production is an international priority nowadays. The objective of this study was to identify the environmental consequences of feedstock selection in biogas production. Two real biogas plants were assessed and compared from a life cycle perspective. Plant A performs the co-digestion of energy crops (78%) and animal waste (22%) while Plant B consumes energy crops (4%), food waste (29%) and animal manure (67%). According to the results, electricity production from biogas implied lower impacts in climate change compared to the existing electric mix. Maize silage (650 Nm3 /TVSfed) and food waste (660 Nm3 /TVSfed) appeared as an interesting source of bioenergy. However, the cultivation of energy crops was identified as the main hotspot in Plant A. Finally, the use of organic substrates with lower energy potential and high nutrients concentration such as animal manure (450 Nm3 /TVSfed) produced higher amounts of digestate, producing impacts in acidification and eutrophication categories. In order to improve the environmental sustainability of bioenergy, specific guideless should be established to achieve harmonised life cycle studies. In addition, environmental policies should promote the use of waste streams and prevent the use of energy crops as well as include goals related with acidification and eutrophication impacts.