Stabilization of soil organic carbon (SOC) against microbial decomposition depends on several soil properties, including the soil weathering stage and the mineralogy of parent material. As such, tropical SOC stabilization mechanisms likely differ from those in temperate soils due to contrasting soil development. To better understand these mechanisms, we investigated SOC dynamics at three soil depths under pristine tropical African mountain forest along a geochemical gradient from mafic to felsic and a topographic gradient covering plateau, slope and valley positions. To do so, we conducted a series of soil C fractionation experiments in combination with an analysis of the geochemical composition of soil and a sequential extraction of pedogenic oxides. Relationships between our target and predicting variables were investigated using a combination of regression analyses and dimension reduction. Here, we show that reactive secondary mineral phases drive SOC properties and stabilization mechanisms together with, and sometimes more strongly than, other mechanisms such as aggregation or C stabilization by clay content. Key mineral stabilization mechanisms for SOC were strongly related to soil geochemistry, differing across the study regions. These findings were independent of topography in the absence of detectable erosion processes. Instead, fluvial dynamics and changes in soil moisture conditions had a secondary control on SOC dynamics in valley positions, leading to higher SOC stocks there than at the non-valley positions. At several sites, we also detected fossil organic carbon (FOC), which is characterized by high C=N ratios and depletion of N. FOC constitutes up to 52.013.2% of total SOC stock in the C-depleted subsoil. Interestingly, total SOC stocks for these soils did not exceed those of sites without FOC. Additionally, FOC decreased strongly towards more shallow soil depths, indicating decomposability of FOC by microbial communities under more fertile conditions. Regression models, considering depth intervals of 0–10, 30–40 and 60–70 cm, showed that variables affiliated with soil weathering, parent material geochemistry and soil fertility, together with soil depth, explained up to 75% of the variability of SOC stocks and 114C. Furthermore, the same variables explain 44% of the variability in the relative abundance of C associated with microaggregates vs. free-silt- and-clay-associated C fractions. However, geochemical variables gained or retained importance for explaining SOC target variables when controlling for soil depth. We conclude that despite long-lasting weathering, geochemical properties of soil parent material leave a footprint in tropical soils that affects SOC stocks and mineral-related C stabilization mechanisms. While identified stabilization mechanisms and controls are similar to less weathered soils in other climate zones, their relative importance is markedly different in the tropical soils investigated.