The agro-ecosystem model Daisy was used to explore the long-term fate of nitrogen (N) after land application of compost and digestate (based on source separated organic municipal solid waste (MSW)). The cumulative crop N yield response and emissions for mineral fertilizer (MF), anaerobically digested organic waste (MSW-D), and composted organic waste (MSW-C) were derived by fitting a linear mixed model to the outcomes of the simulations. The non-linearity of crop N yield responses and emission responses to increasing N fertilizer application was addressed by dividing these responses into high and low crop response conditions. The crop N yield response and five emission pathways (NO3 − leaching to groundwater, NO3 − and NH4 + loss to surface water, and NH3 and N2O emissions into the atmosphere) were quantified as environmental inventory factors, which were calculated for both high and low response conditions. The crop N yield response cumulated over time from the application of N fertilizer almost levelled out for MF within 3 to 5 years after application, while it increased over a time period of 100 years for MSW-C. In addition, MSW-D showed features of both MF and MSW-C, a steep rise in crop N yield response due to high inorganic N content and a gradual increase thereafter, due to the slow mineralization of organic N. Overall, 52–69 % of N applied as MF was up-taken by plant biomass, while plant uptakes of 15–28 % by MSW-D and 19–29 % by MSW-C were measured under high response conditions. When the N fertilizer application rate exceeded the rate of plant uptake, the rate of N utilization dropped by 80–90 % for MF, albeit to lesser degree for MSW-D and MSW-C. The simulations showed that emissions to the environment from organic fertilizers took place over a longer time and omission of the longs-term effects could result in underestimation of potential impacts to the environment. As well as the time scope of assessment, local conditions were determining the N emissions. For the N2O emission, there were very small differences between high and low response conditions for organic fertilizer. The N2O emission factors varied for 1.8–3.0 % for MSW-D and 1.7–5.1 % for MSW-C. For NO3 − leaching to groundwater, there were large differences between high and low response conditions. For high response conditions, the emission factors varied from 6 to 39, 17 to 68, and 9 to 59 of input N from the application of MF, MSW-D, and MSW-C, respectively. Under low response conditions, much higher leaching emission factors were estimated ranging from 21 to 61 % for MF, 20 to 73 % for MSW-D, and 11 to 66 % for MSW-C.