Human activities have greatly increased the availability of biologically active forms of nutrients [e.g., nitrogen (N), phosphorous (P), potassium (K), magnesium (Mg)] in many soil ecosystems worldwide. Multi-nutrient fertilization strongly increases plant productivity but may also alter the storage of carbon (C) in soil, which represents the largest terrestrial pool of organic C. Despite this issue is important from a global change perspective, key questions remain on how the single addition of N or the combination of N with other nutrients might affect C sequestration in human-managed soils. Here, we use a 19-year old nutrient addition experiment on a permanent grassland to test for nutrient-induced effects on soil C sequestration. We show that combined NPKMg additions to permanent grassland have ‘constrained’ soil C sequestration to levels similar to unfertilized plots whereas the single addition of N significantly enhanced soil C stocks (N-only fertilized soils store, on average, 11 t C ha−1 more than unfertilized soils). These results were consistent across grazing and liming treatments suggesting that whilst multi-nutrient additions increase plant productivity, soil C sequestration is increased by N-only additions. The positive N-only effect on soil C content was not related to changes in plant species diversity or to the functional composition of the plant community. N-only fertilized grasslands show, however, increases in total root mass and the accumulation of organic matter detritus in topsoils. Finally, soils receiving any N addition (N only or N in combination with other nutrients) were associated with high N losses. Overall, our results demonstrate that nutrient fertilization remains an important global change driver of ecosystem functioning, which can strongly affect the long-term sustainability of grassland soil ecosystems (e.g., soils ability to deliver multiple ecosystem services).