BACKGROUND Since the 1990's, afforestation programs in the páramo have been implemented to offset carbon emissions through carbon sequestration, mainly using pine plantations. However, several studies have indicated that after the establishment of pine plantations in grasslands, there is an alteration of carbon pools including a decrease of the soil organic carbon (SOC) pool. The aim of this study is to investigate the impact of the establishment of pine plantations on the carbon stocks in different altitudes of the páramo ecosystem of South Ecuador. RESULTS At seven locations within an elevational gradient from 2780 to 3760 m a.s.l., we measured and compared carbon stocks of three types of land use: natural grassland, grazed páramo, and Pinus patula Schlltdl. & Cham. plantation sites. For a more accurate estimation of pine tree carbon, we developed our own allometric equations. There were significant (p < 0.05) differences between the amounts of carbon stored in the carbon pools aboveground and belowground for the three types of land use. In most of the locations, pine plantations revealed the highest amounts of aboveground and belowground carbon (55.4 and 6.9 tC/ha) followed by natural grassland (23.1 and 2.7 tC/ha) and grazed páramo sites (9.1 and 1.5 tC/ha). Concerning the SOC pools, most of the locations revealed significant lower values of plantations' SOC in comparison to natural grassland and grazed páramo sites. Higher elevation was associated with lower amounts of pines' biomass. CONCLUSIONS Even though plantations store high amounts of carbon, natural páramo grassland can also store substantial amounts above and belowground, without negatively affecting the soils and putting other páramo ecosystem services at risk. Consequently, plans for afforestation in the páramo should be assessed case by case, considering not only the limiting factor of elevation, but also the site quality especially affected by the type of previous land use.