This study investigated the impact of regional land abandonment in northeast Portugal. It specifically focused on carbon sequestration opportunities in the Upper Sabor River Watershed, situated in the northeast of Portugal, amidst agricultural land abandonment. The study involved mapping the distribution of soil organic carbon (SOC) across four soil layers (0–5 cm, 5–10 cm, 10–20 cm, and 20–30 cm) at 120 sampling points. The quantification of SOC storage (measured in Mg C ha−1) allowed for an analysis of its relationship with various landscape characteristics, including elevation, land use and land cover (LULC), normalized difference vegetation index (NDVI), modified soil-adjusted vegetation index (MSAVI), topographic wetness index (TWI), and erosion risk (ER). Six statistical tests were employed, including multivariate approaches like Cubist and Random Forest, within different scenarios to assess carbon distribution within the watershed’s soils. These modeling results were then utilized to propose strategies aimed at enhancing soil carbon storage. Notably, a significant discrepancy was observed in the carbon content between areas at higher elevations (>1000 m) and those at lower elevations (<800 m). Additionally, the study found that the amount of carbon stored in agricultural soils was often significantly lower than in other land use categories, including forests, mountain herbaceous vegetation, pasture, and shrub communities. Analyzing bi- and multivariate scenarios, it was determined that the scenario with the greatest number of independent variables (set 6) yielded the lowest RMSE (root mean squared error), serving as a key indicator for evaluating predicted values against observed values. However, it is important to note that the independent variables used in set 4 (elevation, LULC, and NDVI) had reasonably similar values. Ultimately, the spatialization of the model from scenario 6 provided actionable insights for soil carbon conservation and enhancement across three distinct elevation levels.