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• Models performed better in simulating winter wheat and pea compared to sugar beet. • Models performed better in simulating plant N variables compared to soil N variables. • Multi-model ensemble well predicted aboveground biomass, yield, N uptake and N export. • Multi-model ensemble well predicted CC effects on N mineralization and N leaching. Modelling N transformations within cropping systems is crucial for N management optimization in order to increase N use efficiency and reduce N losses. Such modelling remains challenging because of the complexity of N cycling in soil–plant systems. In the current study, the uncertainties of six widely used process-based models (PBMs), including APSIM, CROPSYST, DAISY, FASSET, HERMES and STICS, were tested in simulating different N managements (catch crops (CC) and different N fertilizer rates) in 12-year rotations in Western Europe. Winter wheat, sugar beet and pea were the main crops, and radish was the main CC in the tested systems. Our results showed that PBMs simulated yield, aboveground biomass, N export and N uptake well with low RMSE values, except for sugar beet, which was generally less well parameterized. Moreover, PBMs provided more accurate crop simulations (i.e. N export and N uptake) compared to simulations of soil (N mineralization and soil mineral N (SMN)) and environmental variables (N leaching). The use of multi-model ensemble mean or median of four PBMs significantly reduced the mean absolute percentage error (MAPE) between simulations and observations to less than 15% for yield, aboveground biomass, N export and N uptake. Multi-model ensemble also significantly reduced the MAPE for net N mineralization and annual N leaching to around 15%, while it was larger than 20% for SMN. Generally, PBMs well simulated the CC effects on N fluxes, i.e. increasing N mineralization and reducing N leaching in both short-term and long-term, and all PBMs correctly predicted the effects of the reduced N rate on all measured variables in the study. The uncertainties of multi-model ensemble for N mineralization, SMN and N leaching were larger, mainly because these variables are influenced by plant-soil interactions and subject to cumulative long-term effects in crop rotations, which makes them more difficult to simulate. Large differences existed between individual PBMs due to the differences in formalisms for describing N processes in soil–plant systems, the skills of modelers and the model calibration level. In addition, the model performance also depended on the simulated variables, for instance, HERMES and FASSET performed better for yield and crop biomass, APSIM, DAISY and STICS performed better for N export and N uptake, STICS provided best simulation for SMN and N leaching among the six individual PBMs in the study, but all PBMs met difficulties to well predict either average or variance of soil N mineralization. Our results showed that better calibration for soil N variables is needed to improve model predictions of N cycling in order to optimize N management in crop rotations. [ABSTRACT FROM AUTHOR]