Tropical forests represent the largest store of terrestrial biomass carbon (C) on earth and contribute over-proportionally to global terrestrial net primary productivity (NPP). How climate change is affecting NPP and C allocation to tree components in forests is not well understood. This is true for tropical forests, but particularly for African tropical forests. Studying forest ecosystems along elevation and related temperature and moisture gradients is one possible approach to address this question. However, the inclusion of belowground productivity data in such studies is scarce. On Mt. Kilimanjaro (Tanzania), we studied aboveground (wood increment, litter fall) and belowground (fine and coarse root) NPP along three elevation transects (c. 1800–3900 m a.s.l.) across four tropical montane forest types to derive C allocation to the major tree components. Total NPP declined continuously with elevation from 8.5 to 2.8 Mg C ha−1 year−1 due to significant decline in aboveground NPP, while fine root productivity (sequential coring approach) remained unvaried with around 2 Mg C ha−1 year−1, indicating a marked shift in C allocation to belowground components with elevation. The C and N fluxes to the soil via root litter were far more important than leaf litter inputs in the subalpine Erica forest. Thus, the shift of C allocation to belowground organs with elevation at Mt. Kilimanjaro and other tropical forests suggests increasing nitrogen limitation of aboveground tree growth at higher elevations. Our results show that studying fine root productivity is crucial to understand climate effects on the carbon cycle in tropical forests.