The lack of field-based data in the tropics limits our mechanistic understanding of the drivers of net primary productivity (NPP) and allocation. Specifically, the role of local edaphic factors – such as soil parent material and topography controlling soil fertility as well as water and nutrient fluxes – remains unclear and introduces substantial uncertainty in understanding net ecosystem productivity and carbon (C) stocks. Using a combination of vegetation growth monitoring and soil geochemical properties, we found that soil fertility parameters reflecting the local parent material are the main drivers of NPP and C allocation patterns in tropical montane forests, resulting in significant differences in below- to aboveground biomass components across geochemical (soil) regions. Topography did not constrain the variability in C allocation and NPP. Soil organic C stocks showed no relation to C input in tropical forests. Instead, plant C input seemingly exceeded the maximum potential of these soils to stabilize C. We conclude that, even after many millennia of weathering and the presence of deeply developed soils, above- and belowground C allocation in tropical forests, as well as soil C stocks, vary substantially due to the geochemical properties that soils inherit from parent material.