Soil organic carbon (SOC) is a crucial component of the planet and is essential for agriculture development. Our region is known for its livestock and agricultural activities. Hence, understanding the spatial distribution of SOC is crucial for sustainable land management of soils in the mountain ecosystems in the Andes. The methodology consisted of obtaining 53 soil samples from depths of 0 to 105 cm, which were analyzed to obtain SOC (Kg/m2) and organic matter (OM) (%). Ordinary kriging, a geostatistical method, was used to determine SOC. Pearson’s statistical method was applied to determine the association between SOC and precipitation, temperature, altitude, and organic matter and gave acceptable correlations of 0.38, −0.32, 0.40, and 0.59. These results were used to apply weighting criteria for climatological and environmental variables. The weighted overlay tool was used for modeling and mapping the spatial variability of SOC. The estimated spatial distribution of SOC in the micro-watershed reveals an increasing trend from south to north, specifically within the 0–20 cm depth profile. The study confirmed through the spatial analysis that regions with intensive agriculture have low reserves (<3 Kg/m2) of SOC, and areas without agricultural activity but with grazing have average resources of 3 Kg/m2 to 5 Kg/m2 of SOC. Finally, in the upper micro-watersheds where there is no agricultural activity, the reserves are high (5 Kg/m2 to 6.8 Kg/m2). Accordingly, we can promote sustainable and responsible land use practices that support long-term productivity, environmental protection, and societal well-being by prioritizing efficient land utilization, soil conservation, biodiversity conservation, land restoration, and informed land use planning in the high Andean ecosystem of Puno–Peru.