Savanna ecosystems are increasingly pressured by climate and land-use changes, especially around populous areas such as the Mt. Kilimanjaro region. Savanna vegetation consists of grassland with isolated trees or tree groups and is therefore characterized by high spatial variation and patchiness of canopy cover and aboveground biomass. Both are major regulators for soil ecological properties and soil-atmospheric trace gas exchange (CO2, N2O, CH4), especially in water-limited environments. Our objectives were to determine spatial trends in soil properties and trace gas fluxes during the dry season and to relate above- and belowground processes and attributes. We selected a Savanna plain with vertic soil properties, south east of Mt. Kilimanjaro. Three trees were chosen from each of the two most dominant species: the legume Acacia nilotica and the non-legume Balanites aegyptiaca. For each tree, we selected one transect with nine sampling points, up to a distance of 4 times the crown radius from the stem. At each sampling point, we measured carbon (C) and nitrogen (N) content, δ13C of soil (0–10, 10–30 cm depth) and in plant biomass, soil C and N pools, water content, available nutrients, cation exchange capacity (CEC), temperature, pH, as well as root biomass and greenhouse-gas exchange. Tree species had no effect on soil parameters and gas fluxes under the crown. CEC, C, and N pools decreased up to 50% outside the crown-covered area. Tree leaf litter had a far lower C:N ratio than litter of the C4 grasses. δ13C in soil under the crown shifted about 15% in the direction of tree leaf litter δ13C compared to soil in open area reflecting the tree litter contribution to soil organic matter. The microbial C:N ratio and CO2 efflux were about 30% higher in the open area and strongly dependent on mineral N availability. This indicates N limitation and low microbial C use efficiency in the soil of open grassland areas. We conclude that the spatial structure of aboveground biomass in savanna ecosystems leads to a spatial redistribution of nutrients and thus C mineralization and sequestration. Therefore, the capability of savanna ecosystems to act as C sinks is both directly and indirectly dependent on the abundance of trees, regardless of their N-fixing status.