A major future challenge in agriculture is to reduce the use of new reactive nitrogen (N) while maintaining or increasing productivity without causing a negative N balance in cropping systems. We investigated if strategic management of internal biomass N resources (green manure ley, crop residues and cover crops) within an organic crop rotation of six main crops, could maintain the N balance. Two years of measurements in the field experiment in southern Sweden were used to compare three biomass management strategies: anaerobic digestion of ensiled biomass and application of the digestate to the non-legume crops (AD), biomass redistribution as silage to non-legume crops (BR), and leaving the biomass in situ (IS). Neither aboveground crop N content from soil, nor the proportion of N derived from N2 fixation in legumes were influenced by biomass management treatment. On the other hand, the allocation of N-rich silage and digestate to non-legume crops resulted in higher N2 fixation in AD and BR (57 and 58 kg ha−1 year−1), compared to IS (33 kg ha−1 year−1) in the second study year. The N balance ranged between − 9.9 and 24 kg N ha−1, with more positive budgets in AD and BR than in IS. The storage of biomass for reallocation in spring led to an increasing accumulation of N in the BR and AD systems from one year to another. These strategies also provide an opportunity to supply the crop with the N when most needed, thereby potentially decreasing the risk of N losses during winter. © 2018, The Author(s).