Nitrogen (N) and carbon (C) cycles are closely linked in organic farming systems. Use of residues for biogas digestion may reduce N-losses and lead to higher farmland productivity. However, digestion is connected to large losses of organic C. It is the purpose of this paper (1) to compare farming systems based on liquid slurry and solid farmyard manure regarding the N, C and organic dry matter (ODM) inputs and flows, (2) to analyse the effect of digestion on soil N, C and ODM inputs and flows within the cropping system, (3) to assess the effects of organic manure management on biological N2 fixation (BNF), and (4) to assess the effect of biogas digestion on the sustainability of the cropping systems in terms of N and C budgets. The BNF by clover/grass-leys was the most important single N input, followed by the BNF supplied by legume cover cropping. Growth of crops in organic farming systems is very often N limited, and not limited by the soil C inputs. However, balances of N inputs showed that the implemented organic farming systems have the potential to supply high amounts of N to meet crop N demand. The level of plant available N to non-legume main crops was much lower, in comparison to the total N inputs. Reasons were the non-synchronized timing of N mineralization and crop N demand, the high unproductive gaseous N losses and an unfocussed allocation in space and time of the circulating N within the crop rotation (e.g. allocation of immobile manures to legumes or of mobile manures to cover crops). Simultaneously, organic cropping systems very often showed large C surpluses, which may be potentially increased the N shortage due to the immobilization of N. Soil organic matter supply and soil humus balance (a balance sheet calculated from factors describing the cultivation effects on humus increasing and humus depleting crops, and organic manure application) were higher in cropping systems based on liquid slurry than in those based on solid farmyard manure (+19%). Simultaneously, soil N surplus was higher due to lower gaseous N losses (+14%). Biogas digestion of slurry had only a very slight effect on both the soil N and the soil C budget. The effect on the N budget was also slight if the liquid slurry was stored in closed repositories. Digestion of residues like slurry, crop residues and cover crops reduced in a mixed farming system the soil C supply unilaterally (approximately −33%), and increased the amounts of readily available N (approximately +70–75%). The long-term challenge for organic farming systems is to find instruments that reduce N losses to a minimum, to keep the most limiting fraction of N (ammonia-N) within the system, and to enhance the direct manuring effect of the available manures to non-legume main crops.