Carbon sequestration in agricultural soils is increasingly seen as an effective way to mitigate climate change. Soil organic carbon also plays a crucial role in maintaining soil fertility, water retention, and nutrient cycling and thus is a key element of soil health. However, the frequent use of high amounts of organic fertilizers increases the stored (total) nitrogen pool and subsequent mineralization of soil organic matter contributes to leaching of nitrates into groundwater, degrading drinking water quality and ecosystems. While increasing soil organic carbon can lead to improved soil fertility and water retention, high levels of soil organic carbon, given the right conditions, can lead to increased microbial activity, which can increase nitrogen mineralization and intensify nitrate leaching. In recent studies, it has been shown that nitrate leaching is often largely fed from the soil reserves of organic matter. Furthermore, the composition of humus can vary depending on the source material used for organic fertilization and thus affects subsequent decomposition rate, leading to differences in nutrient availability and stability. Therefore, management practices that promote carbon storage via humus accumulation should be carefully balanced with measures to prevent excessive build up and nitrate losses to ensure optimal soil function and health. The trade-off between carbon storage and nitrate pollution highlights the need for site-adapted approaches that consider both factors simultaneously, while providing the base for crop production. Traditional site-adapted approaches such as crop rotation, cover cropping, and organic amendments have been shown to increase soil organic carbon while reducing nitrogen leaching. Additionally, the use of site-adapted fertilizer recommendations and precision agriculture tools such as soil- and model-based fertilizer recommendations, variable-rate fertilizer application and soil mapping can help optimize nitrogen fertilizer application to maximize yield while minimizing nitrogen leaching and other losses. Understanding the role of mineralization in the seasonal nitrogen supply and matching it with the crop nitrogen demand is of fundamental importance for balancing strategies. In conclusion, increasing soil organic carbon is an important strategy for mitigating climate change and improving soil fertility and crop production, but must be balanced with efforts to maintain water quality and prevent soil degradation. Site-adapted approaches that consider environmental factors such as soil type, topography, water and nutrient availability can help optimize fertilizer management practices to achieve both goals simultaneously. By balancing soil fertility and soil services, we can achieve systems that benefit both the environment and crop production.