This study analyzed the ecological factors influencing soil degradation in the Atacora Mountains in northern Benin, which harbor two endemic species, Thunbergia atacorensis and Ipomoea beninensis. Data were collected along line transects from plain to summit within 22 plots of 30 m × 30 m. Indicators of physical soil degradation (extent of organic layer, color of topsoil, compactness of soil, presence and extent of rills, and occurrence of sheet erosion) and environmental factors (canopy and ground cover, topography, occurrence of flooding, and slope) were assessed. Cluster analysis identified 4 soil degradation classes: light, moderate, high, and extreme. Discriminant and multivariate variance analyses identified canopy and ground cover as the 2 main ecological drivers of soil degradation. Plant, litter, and stone cover were found to decrease as soil degradation increased. The parts of the Atacora Mountains with high elevation and steep slope were found to be less degraded than areas with low slopes, which are easily accessible for human activities. Policies to mitigate soil degradation should prioritize practices with low impact on vegetation cover and promote soil protection practices such as tree planting and mulching.