Organic fertilizers often contribute to nitrate (NO3−) leaching and impair drinking water quality, because the mineralization of applied organic nitrogen (N) is often asynchronous with crop N uptake. Crop yield, crop N uptake, seepage water and NO3− leaching were investigated in a lysimeter facility (Zurich, Switzerland) under temperate climate conditions during two consecutive four-year organically managed crop rotations. The study compared untreated cattle slurry, anaerobically digested slurry, liquid digestate from a non-agricultural biogas plant and a zero-N fertilization control. The ammonium N (NH4-N) fraction of the organic fertilizers was labeled with 15N tracer to investigate the fate of NH4-N in the plant-soil–water system. Organic fertilization significantly increased crop yields and N uptake, with no differences among organic fertilizers, despite the higher NH4-N proportion of the digestates. Mean annual NO3− leaching was low (12–18 kg N ha−1) and was not increased by organic fertilization, indicating that N inputs were balanced by crop N uptake. Digestates did not differ from untreated cattle slurry in NO3− leaching. Higher modeled ammonia (NH3) emissions of digestates suggest that N losses may occur primarily via NH3 volatilization rather than NO3− leaching. The 15N recovery showed ~1% of the applied NH4-N was lost through NO3− leaching, whereas 23–31% was recovered in crops, and 18–23% remained in the topsoil. These results highlight the importance of crop N uptake and the role of the soil as a long-term reservoir for fertilizer-derived N, with direct NO3− leaching from the NH4-N fraction of organic fertilizers playing only a minor role.