Recently, many countries have introduced policies that promote sustainable agricultural practices, such as reducing synthetic nitrogen fertiliser and promoting diversified crop rotation. While such management changes might represent an opportunity for the agricultural sector to mitigate the impacts of climate change through carbon (C) sequestration in soils, there are still uncertainties due to the scarcity of reliable long-term data to prove this assumption. In this study, we applied the DayCent model using empirical data from a farm-scale study and an experimental trial study at Nafferton farm in the UK, to assess the long-term effects of contrasting agricultural systems (conventional vs. organic), grazing regimes (non-grazed vs. grazed), arable systems with ley phases, mineral vs. compost fertility sources and conventional vs. organic crop rotation on soil C stocks (0-0.20 m depth). The simulations showed that grazing and higher ley time proportions can increase soil C stocks for a period of at least 30 years, regardless of the agricultural system used (average increase in rates of 0.25 ± 0.02 Mg ha −1 yr −1). Compost fertiliser promoted soil C accumulation for the same period (average increase in rates of 0.3 Mg ha −1 yr −1), but its magnitude was dependent on the choice of crops in the rotation. However, ley time proportions higher than 40% of the full crop rotation did not improve soil C accumulation further. We conclude that the DayCent model can be used to identify the quantity of and the effective period for which management practices can be used to target mitigation efforts, but the balance between sustainability and productivity aspects warrants further research.