The utilization of agricultural biomass for anaerobic digestion is increasing in Germany since the first version of the Renewable Energies Sources Act (EEG) in 2000. Main products of this conversion process are biogas and digestate, whereby the biogas is mainly used for generation of heat and electricity in combined heat and power plants (CHP). This study investigated the potential environmental impact of anaerobic digestion processes with different agricultural substrates by the life cycle assessment (LCA) method. It focuses on liquid manure and energy crops as feedstock on the one hand and a comparison of four virtual model plants on the other hand. Besides global warming potential (GWP), the impact categories eutrophication potential (EP) and acidification potential (AP) are presented in this work. The results show that greenhouse gas emissions can be reduced with anaerobic digestion of liquid manure as well as energy crops, particularly when digestate storage tanks are gas-tight. When energy crops are fermented together with liquid manure, the biggest credit for the avoidance of greenhouse gas emissions was given for the generation of electricity. The results differ from those of GWP when looking at the AP and the EP. These impact categories show similar results with a reduction of emissions for liquid manure in mono-digestion but increasing emissions for digestion of energy crops together with 0–35% liquid manure.