The SPACSYS model simulated wheat and maize yields accurately.
The SPACSYS model adequately simulated the dynamics of SOC and SN stocks.
Fertilisation and climate change positively impact on crop yields and SOC stock.
Soil nitrogen stock decreases by 3–14% under the RCP8.5 scenario by 2100.
Mineral fertilisers plus manure led to a higher soil respiration and N losses.