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To improve agricultural sustainability, alternative cultivation methods and assessment tools need to be developed. Integrating service crops (SC) can potentially increase cropping system multifunctionality and mitigate negative climate and environmental impacts of agriculture. (1) Calibrate oats, winter wheat and red clover SC, grown as sole crops and intercrops, in the cropping system model APSIM NG for northern Europe climate conditions. (2) Use the calibrated crop modules to assess ecosystem processes from an intercropping system. (3) Discuss the role of mechanistic crop models in assessing ecosystem services and disservices from complex cropping systems. The crops were calibrated with data from an oats-winter wheat cropping sequence at two field sites. Thirty weather datasets were created from historical weather data to generate weather-dependent variability in crop performance and related processes. The assessment compared two scenarios, with or without an intercropped red clover SC sown in oats and terminated the following spring in winter wheat. Outputs representing processes related to important ecosystem services were extracted from the simulations. Calibration of the three crops resulted in satisfactory biomass levels at the end of the growing season. Including a SC reduced oat yield, but increased winter wheat yield in two-thirds of simulations. Model outputs showed that including a SC resulted in 33–79% more fresh soil organic carbon, depending on site, compared with no SC. Nitrogen (N) uptake by both crops was highest in the SC scenario. In oats, N losses did not differ between the two scenarios, while in winter wheat the SC scenario had approximately 50% lower N leaching losses and 30% higher gaseous N emissions. However, in the fallow period from winter wheat harvest through to spring, both types of N losses were elevated in the SC scenario. The SC scenario had only a minor effect on water dynamics, causing a small reduction in soil water content. In this paper we give an example of how APSIM NG can be used to assess ecosystem services from complex agricultural systems using a case study with intercropping of cereals and leguminous SCs. APSIM NG was useful in providing a holistic assessment, and we show that intercropping with a SC can improve cropping system performance and reduce negative impacts, but long-term strategic management of N is required to prevent increased losses. To further improve simulation of intercrops more accurate simulation of early growth is needed for all crops included. [Display omitted] • Crop modules for oats, winter wheat and red clover were calibrated to simulate intercrops in Sweden in APSIM NG. • Effects of intercropping cereals (oats-winter wheat) and a legume service crop on cereals and soil processes were assessed. • Calibration resulted in satisfactory end-biomass, but poor simulation of biomass during leaf development and tillering. • Intercropping with a service crop had positive effects from an ecosystem service perspective. • Drawbacks were elevated N losses in winter wheat and fallow, indicating a need for long-term N management. [ABSTRACT FROM AUTHOR]