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Soil organic carbon (SOC) constitutes the largest terrestrial C stock, particularly in the Andosols of volcanic areas. Quantitative information on distribution of SOC stocks is needed to construct a baseline for studying temporal changes in SOC. The spatial variation of soil short-range-order minerals such as allophane usually explains the variability of topsoil SOC contents, but SOC data for deeper soil layers are needed. We found that within a 1 km2 Costa Rican basin covered by coffee agroforestry, SOC stocks in the upper 200 cm of soil were highly variable (24 to 72 kg C m−2). Topsoil SOC stocks were not correlated with SOC stocks present in deeper layers. Diffuse-reflectance mid-infrared (MIR) spectroscopy made possible the analysis of a large number of samples (69 soil profiles, i.e. 598 soil samples) for ammonium-oxalate and sodium-pyrophosphate-extractable forms of Al, Fe, and Si, as well as SOC content and bulk density. Using the MIR spectra, we identified two different soil materials, which were identified as allophanic and halloysitic soil material. Allophanic soil occurred on top of the halloysitic soil. The thickness of the allophanic soil material, rich in SRO minerals and related to a young andic A horizon, explained the variability of SOC. This study illustrates that knowledge of topography and pedogenesis is needed to understand and extrapolate the distribution of SOC stocks at landscape scales.