A large source of uncertainty in present understanding of the global carbon cycle is the distribution and dynamics of the soil organic carbon reservoir. Most of the organic carbon in soils is degraded to inorganic forms slowly, on timescales from centuries to millennia. Soil minerals are known to play a stabilizing role, but how spatial and temporal variation in soil mineralogy controls the quantity and turnover of long-residence-time organic carbon is not well known. Here we use radiocarbon analyses to explore interactions between soil mineralogy and soil organic carbon along two natural gradients—of soil-age and of climate—in volcanic soil environments. During the first ∼150,000 years of soil development, the volcanic parent material weathered to metastable, non-crystalline minerals. Thereafter, the amount of non-crystalline minerals declined, and more stable crystalline minerals accumulated. Soil organic carbon content followed a similar trend, accumulating to a maximum after 150,000 years, and then decreasing by 50% over the next four million years. A positive relationship between non-crystalline minerals and organic carbon was also observed in soils through the climate gradient, indicating that the accumulation and subsequent loss of organic matter were largely driven by changes in the millennial scale cycling of mineral-stabilized carbon, rather than by changes in the amount of fast-cycling organic matter or in net primary productivity. Soil mineralogy is therefore important in determining the quantity of organic carbon stored in soil, its turnover time, and atmosphere–ecosystem carbon fluxes during long-term soil development; this conclusion should be generalizable at least to other humid environments.