We analysed the environmental impacts of three biogas systems based on dairy manure, sorghum and maize. The geographical scope of the analysis is the Po valley, in Italy. The anaerobic digestion of manure guarantees high GHG (Green House Gases) savings thanks to the avoided emissions from the traditional storage and management of raw manure as organic fertiliser. GHG emissions for maize and sorghum-based systems, on the other hand, are similar to those of the Italian electricity mix. In crop-based systems, the plants with open-tank storage of digestate emit 50% more GHG than those with gas-tight tanks. In all the environmental impact categories analysed (acidification, particulate matter emissions, and eutrophication), energy crops based systems have much higher impacts than the Italian electricity mix. Maize-based systems cause higher impacts than sorghum, due to more intensive cultivation. Manure-based pathways have always lower impacts than the energy crops based pathways, however, all biogas systems cause much higher impacts than the current Italian electricity mix. We conclude that manure digestion is the most efficient way to reduce GHG emissions; although there are trade-offs with other local environmental impacts. Biogas production from crops; although not providing environmental benefits per se; may be regarded as an option to facilitate the deployment of manure digestion.