Protected areas are important zones for the conservation of strategic ecosystems that provide environmental services to human populations. The Santuario de Fauna y Flora Iguaque (SFFI) (Boyacá, Colombia) preserves an important area of páramos and andean high-land forests that offer water and other services. Soil organic carbon (SOC) was estimated at a depth of 0–30 cm in the four dominant land uses: (1) natural grasslands prevailingly without trees and shrubs (NSWT), (2) broad-leaved forests with continuous canopy, not on mire (BFCC), (3) open heathlands and moorlands (OMH), and (4) dense heathlands and moorlands (DMH). This classification is based on Corine Land Cover, adapted for Colombia. Land uses did not differ significantly (p > 0.05) in the SOC stock, with values of 139.0, 131.1; 101.1; and 83.0 Mg C/ha in OMH, BFCC, NSWT, and DMH, respectively. In total, SFFI retains 593 Gg C in that soil layer. Projections of effects caused by potential land use changes show that up to 461.0 Gg CO2 could be transferred to the atmosphere if this conservation area is not preserved. SFFI, due to its conservation strategies, allows storing significant amounts of atmospheric carbon and becomes an effective strategy of climate change mitigation.