Savannas are dry tropical biomes characterized by high above- and belowground biomass production, but at the same time there is extensive C loss by fire regimes. Soil-mediated responses are crucial in biogeochemical cycling and the role of soil minerals may be important in controlling organic carbon (OC) storage and stabilization. The objective of this study was to determine OC fractional distribution and saturation capacity in three soil groups (Vertisols, Lixisols, Luvisols) that are characterized by specific and different 1:1 and 2:1 clay mineral dominance. For each soil group, top- and subsoils (0–10 cm, 40–60 cm) were sampled in protected Soudanian savannas across Burkina Faso and fractionated into free and aggregate-occluded particulate organic matter (fPOM, oPOM) and mineral-associated organic matter (mOM). The results showed that oPOM and mOM were significantly affected by soil groups and topsoil/subsoil layers. We consider this to be due to interactions with fine particles (clay, fine and medium silt), the presence of exchangeable Ca and Mg and extractable Al (D) and Fe (D) as revealed by significant positive correlations. We found that oPOM (13–29% of total OC) and mOM < 20 µm (54–76%) were the most important OC pools in these tropical savanna soils. Vertisols exhibited the highest OC contents and held three times more OC in the fine mineral fraction mOM < 20 µm than Lixisols and Luvisols. Luvisols were affected by mineral illuviation processes which lowered their OC contents. Overall, topsoils contained three times higher OC amounts of mOM < 20 µm than subsoils. Indications were found that all investigated topsoils are below OC saturation, likely due to prescribed fire and soil erosion effects, while the OC saturation deficit was important in Vertisols (−49 to −65%) and Lixisols (−41 to −45%). We conclude that tropical savanna soils have a high protective capacity for OC in top- and subsoils but require adequate management in order to increase OC storage.