Few fertilizers are permitted for organic farming, which is a challenge when securing nutrient availability, particularly of nitrogen (N). Digestate from biogas production could be a valuable fertilizer for increasing crop yields, through its high content of plant-available nitrogen (NH4-N), but is rarely used in practice. This study evaluated how anaerobic digestion of manure and use of digestate affected inflows and outflows of nutrients and potentially toxic elements on four organic farms with different solutions for digestate production. Mass flows and element concentrations were documented 3 years on three dairy farms and one crop farm and used for calculating farm budgets. Nitrogen and phosphorus (P) budgets were also calculated for biogas reactor and storage pits on three farms. Nitrogen surplus exhibited large variation (18–87 kg N ha−1 year−1) at farm level, with purchased digestate or poultry manure giving major N inputs. The risk of process losses was high, with up to 40% of N and P in feedstock entering farm biogas reactors not recovered in digestate. The proportion of NH4-N in total N in digestate was slightly higher (2–9%) or lower (37%) than in feedstocks entering farm biogas reactors. Improved stirring in farm biogas reactors and storage pits to decrease N and P sedimentation, particularly when digesting poultry manure, would directly increase digestate value. Two farms purchasing digestate from central biogas plants received a digestate causing significant cadmium inputs. Keeping records on element flows can help to tailor the use of digestate for organic farms to achieve a sustainable use of nutrients.