Our research takes advantage of a historical trend in natural reforestation of abandoned tropical pastures to examine changes in soil carbon (C) during 80 years of secondary forest regrowth. We combined a chronosequence approach with differences in the natural abundance of 13C between C3 (forest) and C4 (pasture) plants to estimate turnover times of C in the bulk soil and in density fractions. Overall, gains in secondary forest C were compensated for by the loss of residual pasture-derived soil C, resulting in no net change in bulk soil C stocks down to 1 m depth over the chronosequence. The free light fraction (LF), representing physically unprotected particulate organic matter, was most sensitive to land-use change. Reforestation replenished C in the free LF that had been depleted during conversion to pastures. Turnover times varied with model choice, but in general, soil C cycling rates were rapid for the 0–10 cm depth, with even the heavy fraction (HF) containing C cycling in decadal time scales. Turnover times of C in the free LF from the 0–10 cm depth were shorter than for the occluded and HFs, highlighting the importance of physical location in the soil matrix for residence time in the soil. The majority of the soil C pool (82±21%) was recovered in the mineral-associated density fraction. Carbon-to-nitrogen ratios and differences in natural abundance 15N of soil organic matter (SOM) showed an increasing degree of decomposition across density fractions with increasing mineral association. Our data show that the physical distribution of C in the soil has a large impact on soil C turnover and the ability of soils to maintain SOM stocks during land-use and land-cover change.