Organic and conventional cropping systems differ in type and amount of nitrogen (N) inputs. In organic cropping only organic fertilizers are permitted, while both organic and mineral fertilizers are used in conventional cropping. Fertilizer type and amount can affect N use efficiency of a cropping system, but contributions via symbiotic N fixation and changes in soil N stocks are rarely quantified based on field data when computing nutrient budgets. We calculated an N budget that accounts for these contributions based on annual data records for a period of 35 years at the Swiss DOK (bio-Dynamic, bio-Organic, Konventionell) field experiment. Here, different organic and conventional cropping systems have been maintained at two fertilization levels: typical for the respective system, and half these doses (low). Controls comprise a conventional treatment receiving solely mineral fertilizers and an unfertilized treatment. At the typical level, average fertilizer N inputs were 93 (bio-dynamic), 96 (bio-organic), and 171 (conventional system) kg N ha−1 yr−1. Nitrogen output via harvested products regularly exceeded N input with fertilizers in all treatments. In each of the 7-year crop rotation periods, legumes (grass-clover ley, intercrops, soybean) were grown in three years. Their symbiotic N fixation was quantified based on 15N studies and legume N yield data. It ranged from 75 to 122 kg N ha−1 per year of the DOK experiment, was slightly reduced under low fertilization and was the main N input for most treatments. Soil surface budgets (sum of N inputs from fertilization, symbiotic fixation, seeds, and deposition minus N outputs via crop harvests) yielded balances from −31 kg N ha−1 yr−1 (in non-fertilized control) to +46 kg N ha−1 yr−1 (conventional system with typical fertilization level). Nitrogen use efficiencies (NUE; N output with harvests as % of sum of N inputs) reached values >100 % in treatments with negative balances while NUE ranged from 85 % to 99 % in treatments with positive balances. Changes in topsoil (0–0.2 m) N stocks over time ranged from −26 to +9 kg N ha−1 yr−1 and declined in both unfertilized and mineral fertilized controls, and in systems receiving animal manure at low fertilization levels. Thus, positive soil surface N balances and animal manure are needed to maintain or increase topsoil N stocks. While NUE was generally high in all cropping systems there remains a trade-off between either soil N mining at higher NUE or potential N loss to the environment at lower NUE.