Soil organic carbon (SOC) and total nitrogen (TN) are key ecological indicators of soil quality in a given landscape. Their status, especially in drought-prone landscapes, is associated mainly with the land-use type and topographic position. This study aimed to clarify the effect of land use and topographic position on SOC and TN stocks to further clarify the ecological processes occurring in the landscape. To analyze the status of SOC and TN, we collected 352 composite soil samples from three depths in the uppermost soil (0–50 cm) in four major land-use types (bushland, cropland, grazing land, and plantation) and three topographic positions (upper, middle, and lower) at three sites: Dibatie (lowland), Aba Gerima (midland), and Guder (highland). Both SOC and TN stocks varied significantly across the land uses, topographic positions, and agro-ecosystems. SOC and TN stocks were significantly higher in bushland (166.22 Mg ha−1) and grazing lands (13.11 Mg ha−1) at Guder. The lowest SOC and TN stocks were observed in cropland (25.97 and 2.14 Mg ha−1) at Aba Gerima, which was mainly attributed to frequent and unmanaged plowing and extensive biomass removal. Compared to other land uses, plantations exhibited lower SOC and TN stocks due to poor undergrowth and overexploitation for charcoal and firewood production. Each of the three sites showed distinct characteristics in both stocks, as indicated by variations in the C/N ratios (11–13 at Guder, 10–21 at Aba Gerima, and 15–18 at Dibatie). Overall, land use was shown to be an important factor influencing the SOC and TN stocks, both within and across agro-ecosystems, whereas the effect of topographic position was more pronounced across agro-ecosystems than within them. Specifically, Aba Gerima had lower SOC and TN stocks due to prolonged cultivation and unsustainable human activities, thus revealing the need for immediate land management interventions, particularly targeting croplands. In a heterogeneous environment such as the Upper Blue Nile basin, proper understanding of the interactions between land use and topographic position and their effect on SOC and TN stock is needed to design proper soil management practices.