This study aimed to develop a comprehensive methodological Model for assessing 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 mountain andean tropical conditions. The model comprises three main components: (1) assessing the hazard of desertification using climatic, geomorphometric, and land cover and use indicators; (2) generating the soil vulnerability index by estimating 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, demonstrated the potential to differentiate areas with varying levels of risk. The analysis identified a clear trend, the medium risk desertification category is the dominant condition in the Amaime river basin, covering a significant area 445.82 km2 (42.7%). In the study was evidenced a high to medium hazard conditions in areas with water deficit for the flat part and slopes greater than 25%. These conditions are mainly found in areas under transitory crops, permanent crops, and pastures with a highly intensive land uses distributed from the western to the northeast sectors in the basin. Additionally, 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.