We compared the soil carbon dynamics between a pine plantation and a secondary forest, both of which originated from the same farmland abandoned in 1976 with the same cropping history and soil conditions, in the wet tropics in Puerto Rico from July 1996 to June 1997. We found that the secondary forest accumulated the heavy-fraction organic carbon (HF-OC) measured by the density fractionation technique, more efficiently than the tree plantation did. Although there was no significant difference in total soil organic carbon (SOC) between the plantation (5.59±0.09 kg m−2) and the secondary forest (5.68±0.16 kg m−2), the proportion of HF-OC carbon to the total SOC was significantly higher in the secondary forest (61%) than in the plantation (45%) (P<0.05). Forest floor mass and aboveground litterfall in the plantation were 168% and 22.8% greater than those in the secondary forest, respectively, while the decomposition rate of leaf litter in the plantation was 23.3% lower than that in the secondary forest. The annual mean soil respirations in the plantation and the secondary forest were 2.32±0.15 and 2.65±0.18 g C m−2 day−1, respectively, with a consistently higher rate in the secondary forest than in the plantation throughout the year. Microbial biomass measured by fumigation–incubation method demonstrated a strong seasonal variation in the secondary forest with 804 mg kg−1 in the wet season and 460 mg kg−1 in the dry season. However, the seasonal change of microbial biomass in the plantation was less significant. Our results suggested that secondary forests could stock more long-term SOC than the plantations in the wet tropics because the naturally generated secondary forest accumulated more HF-OC than the managed plantation.