Soil erosion is a multi-dimension problem that attracted the attention of researchers and planners worldwide. Literature reports, soil conservation strategies should be integrated with the priority assessment to deal with such a problem and taking up a focus according to the priority order. However, in spite of various forms of land and water degradation in Rwanda, a holistic investigation or multi-criteria based watersheds prioritization that integrate various aspects and methods has yet to be assessed. Thus, Nyabarongo River Catchment which is the major river catchment in Rwanda that drains about 33% of the total Rwanda coverage has been selected and sub-watersheds were grouped into three order clusters (C1, C2, and C3) using Hierarchical Cluster Analysis (HCA). The priority assessment was estimated using the combination of Compound parameter index (Ci) and Erosion Hazard Rate Index (EHRI) derived from the Analytical Hierarchy Process (AHP) in Geographic Information System (GIS) using remote sensing, soil and geology data. Based on the literature, the Ci technique, in general, considered four parameters viz. morphometric analysis dimensionally reduced using the Principal Component Analysis (PCA) together with land cover, soil, and geology. Whereas EHRI considered five Erosion Hazard Parameters (EHPs) viz. Soil Loss (SL), Sediment Production Rate (SPR), Sediment Transport Index (STI), Runoff Potential (RP), and Slope. The priority assessment was categorized into High, Moderate, and Low priority classes. The priority assessment based on Ci and EHRI provided the same outcome. They noticed high priority in sub-watersheds under cluster C2 account for (35.94%), those under cluster C3 comprise for (16.27%) were identified as a moderate priority, and sub-watersheds belonging to cluster C1 account for (47.8%) falling under low priority sub-watersheds for conservation measures. Therefore, effective soil conservation measures at a priority basis are needed for sustained productivity while minimizing undesirable effects on the environment.