A comprehensive methodological model was developed for evaluating the risk of desertification and land degradation in Andean mountainous areas (MRDA), as a support for climate-smart sustainability. The conceptual framework was based on the concept of risk and involved structuring the methodological model and adapting biophysical and land-use indicators to estimate the interaction between hazard and vulnerability, which determines the risk of desertification and land degradation in a specific site or region under Andean mountain tropical conditions. The model comprised the following three primary components: (1) evaluating the risk of desertification using climatic, geomorphometric, and land cover and -use indicators, (2) generating the soil vulnerability index by estimating the inherent and dynamic soil quality (exposure, sensitivity, and adaptive capacity indicators), and (3) calculating the desertification risk index. The model was applied and calibrated in a pilot area in the Andean catchment, and the potential for differentiating areas with varying levels of risk was demonstrated. The analysis identified a clear trend, wherein the medium-risk desertification category was the dominant condition in the Amaime River basin, covering a significant area of 445.82 km2 (42.7%). The results evidenced high- to medium-hazard conditions in areas with water deficit for the flat part and slopes > 25%. These conditions are primarily found in areas under transitory crops, permanent crops, and pastures with highly intensive land uses distributed from the western to the northeast sectors in the basin. Furthermore, due to its simplicity, this approach could be used in similar regions in tropical areas to provide information on the progress or status of processes associated with desertification and land degradation.