Soil research in temperate to cool and humid regions has typically focused on acidic soils; there has been relatively little investigation of the effects of calcium carbonate (CaCO3) on unamended soil properties or function in these environments. The object of this study was to characterise the effects of small amounts of CaCO3 on pedogenic trajectories and soil biogeochemistry in a humid subalpine valley of Switzerland. To isolate the influence of CaCO3, six profiles were selected that had developed under almost identical conditions for soil formation, i.e. climate, topography, vegetation structure, time since deglaciation, silicate mineralogy and texture. The main difference between the profiles was that three contained a small quantity of CaCO3 (<6.2%; thereafter, ‘CaCO3-bearing’) while the remaining three contained no detectable CaCO3 (thereafter, ‘CaCO3-free’). The presence of CaCO3 was associated with cascading changes in soil biogeochemistry. These changes included higher pH, an order of magnitude higher extractable Ca and twice as much soil organic carbon (SOC). CaCO3-bearing profiles also displayed a higher proportion of poorly crystalline Fe forms. The higher pH at the CaCO3-bearing site was attributable to the weak buffering provided by CaCO3 dissolution, which in turn maintained the relatively higher extractable Ca. Exchangeable Ca (CaExch) and other reactive Ca forms could help stabilise SOC, contributing to its accumulation through processes such as flocculation and subsequent occlusion within aggregates and/or sorption to mineral surfaces. The increased SOC, CaExch and pH at the CaCO3-bearing site could in turn be inhibiting the crystallisation of disordered Fe forms, but further research is required to confirm this effect and isolate the exact mechanisms. Overall, this study shows that the presence of small amounts of CaCO3 in humid environments has a far-reaching influence on soil biogeochemistry and further supports the idea that indicators of Ca prevalence have the potential to improve regional SOC estimates.