The high-Andean grasslands of Peru provide a wide range of goods and services, not only locally, but also regionally and globally. However, land-use change and global warming are threatening these ecosystems, of which soil organic carbon (SOC) is a key element affecting their sustainability. In this study, we have analyzed the variation of SOC stocks to a depth of 20 cm in 16 paired cropland and grassland sites located in the Sullccapallcca stream micro-watershed (elevation > 3600 m.a.s.l., Ayacucho, Peru). We have also analyzed the environmental controls on the SOC stocks and their variation with land-use change. We found that the studied high-Andean grasslands store high SOC contents (247 Tn SOC ha⁻¹), whose spatial variability was partially explained by the slope of the terrain (r² = 0.26, p < 0.05). Despite the higher NDVI, the conversion of these grasslands into croplands decreased the SOC stock by 39 Tn SOC ha⁻¹ on average, a decrease that was more pronounced when the initial SOC content of the grassland was higher (r² = 0.60, p < 0.05). This study provides the first evidence of the effects of land-use change on the SOC in the region, although the mechanisms involved still need to be investigated.