Variations in the stable isotopic composition of carbon (δ13C) and nitrogen (δ15N) of fresh leaves, litter and topsoils were used to characterize soil organic matter dynamics of twelve tropical ecosystems in the Mount Kilimanjaro region, Tanzania. We studied a total of 60 sites distributed along five individual elevational transects (860–4550ma.s.l.), which define a strong climatic and land use gradient encompassing semi-natural and managed ecosystems. The combined effects of contrasting environmental conditions, vegetation, soil, and management practices had a strong impact on the δ13C and δ15N values observed in the different ecosystems. The relative abundance of C3 and C4 plants greatly determined the δ13C of a given ecosystem. In contrast, δ15N values were largely controlled by land-use intensification and climatic conditions. Both δ15N values and calculated δ15N-based enrichment factors (δ15Nlitter–δ15Nsoil) indicate tightest nitrogen cycling at high-elevation (〉3000ma.s.l.) ecosystems, and more open nitrogen cycling both in grass-dominated and intensively managed cropping systems. The negative correlation of δ15N values with soil nitrogen content and the positive correlation with mean annual temperature suggest reduced mineralisation rates, and thus limited nitrogen availability, at least in high-elevation ecosystems. By contrast, intensively managed systems are characterized by lower soil nitrogen contents and warmer conditions, leading together with nitrogen fertilizer inputs to lower nitrogen retention, and thus, significantly higher soil δ15N values. A simple function driven by soil nitrogen content and mean annual temperature explained 68% of the variability in soil δ15N values across all sites. Based on our results, we suggest that in addition to land use intensification, increasing temperatures in a changing climate may promote soil carbon and nitrogen losses, thus altering the otherwise stable soil organic matter dynamics of Mt. Kilimanjaro’s forest ecosystems.