An indicator of soil fertility is the content of organic matter measured by the share of carbon in the soil, which is negatively affected by many conventional land management practices. As those heavily depend on individual land use decisions, the agent-based model of regional structural change AgriPoliS is applied to assess carbon losses resulting from behaviors and interactions of individual farms. The extended model now considers nitrogen input and the development in soil’s carbon content. Three scenarios are implemented where farms have either to use 7%, 15% or 25% of their land as ecological focus area (EFA). Results show that although carbon losses continue at a slower pace under the 7%-scenario, 25% of the land is to be set aside to stop them completely. However this implies short-term income losses for farmers but better plant resistance and improved soil productivity in the long-run if soil organic matter can be maintained.