This study determined the change and distribution of land-uses/covers along the landscape, and evaluated the nutrient status of the top soil layer in the Lake Kivu Pilot Learning Site (LKPLS) benchmarked micro-catchments. Soil physical and chemical properties were quantified using triplicate soil samples collected from each land-use/cover at two depths (0-15 and 15-30 cm) in three LK PLS Learning Innovation Platform (IP) sites (Bufundi in Uganda, Mupfuni-Shanga in D.R. Congo, Gataraga in Rwanda). Small scale agriculture has increased in all the benchmarked micro-catchments at the expense of other land-uses/covers. In the settlement areas land-use/cover distribution along the landscape varied across sites and countries; the major one being eucalyptus woodlots, wetland, and perennials and annuals crops in Bufundi; annuals and perennials crops in Mupfuni-Shanga; and annuals crops in Gataraga. Perennial crops tended to occur at the footslope and valley bottoms, while the annuals occurred at the upper backslopes and summits. Available P and K were relatively higher and C/N ratio (7.28) was the lowest in Mupfuni Shanga. Annual crops had the lowest available P and N across site ( < 0.05). The key nutrients N, P and K were below the critical values for plant growth for Bufundi.