A life-cycle assessment (LCA) was carried out to compare the environmental performance of different organic cropping systems with and without digestion of slurry and crop residues. The aims of the present study are: (1) to compare the environmental performance of organic farming dairy systems with the currently prevalent animal housing systems [solid farmyard manure (FYM) versus liquid slurry] as the main reference systems; (2) to analyze the effect of the implementation of a biogas digestion system on the consumption of fossil fuels and production of electrical energy; (3) to quantify the effects of the implementation of a biogas digestion system on the environment; and (4) to compare the obtained net energy yields with other means of obtaining energy by using the farmland area. The considered impact categories are greenhouse gas (GHG) balances, acidification, eutrophication and groundwater pollution. LCA results indicated that total emissions in systems based on FYM are much higher than in liquid slurry systems for most of the considered impact categories. The benefits of digestion of stable wastes in comparison with the reference system without digestion are mainly (1) the net reduction of the emissions of GHG and (2) energy recovery from produced biogas, while the disadvantages can be higher emissions of NH3 after spreading. The effects of additional biogas digestion of biomass such as crop residues (e.g., straw of peas and cereals) and cover crops are: (1) an optimization of the N-cycle and therewith higher yields; (2) higher energy production per unit arable land; (3) a further reduction of the GHG balance; but (4) higher N-related environmental burdens like eutrophication and acidification. The offsets of fossil fuel emissions were the largest GHG sink in most of the biogas digestion systems. The inclusion of a biogas plant into organic cropping systems and the use of the available wastes for production of energy largely increased the overall productivity of the farming system and matched very well the basic principles of organic farming such as a high self-sufficiency of the cropping system and reducing as much as possible the environmental impact of farming.