Human pressure on a rugged and fragile landscape can cause land use/cover changes that significantly alter the provision of ecosystem services. Estimating the multiple services, particularly those obtained from agroforestry systems, is seldom attempted. A combined approach of geospatial technology, cross-sectional field investigations, and economic valuation of natural capital was used to develop an ecosystem service valuation (ESV) model to estimate changes in ESV between 1986 and 2015 in southern Ethiopia. Over 120 values were sourced, mainly from an ecosystem service valuation database and allied sources, to establish value coefficients via benefit transfer method. Our 1848 km2 study landscape, with eight land use categories, yielded an annual total ESV of $129 × 106 in 1986 and $147 × 106 in 2015, a 14.2% ($18.3 million) increase in three decades, showing its relative resilience. Yet we observed losses of natural vegetation classes whose area and/or value coefficients were too small to offset their increased value from expanding agroforestry and wetland/marshes, which have the largest cover share and highest economic value, respectively. Appreciating the unique features of agroforests, we strongly recommend that their economic value is studied as a separate ecosystem for further valuation accuracy improvement.