Summary 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.