Soil organic matter is a key factor in the global carbon cycle, but the magnitude and the direction of the change in soil carbon after afforestation with Eucalyptus in the tropics is still a matter of controversy. The objective of this work was to understand the dynamics of soil carbon in intensively managed Eucalyptus plantations after the afforestation of a native savannah. The isotopic composition (δ) of soil carbon (C) and soil CO2 efflux (F) were measured on a four-age chronosequence of Eucalyptus and on an adjacent savannah. δ F was used to partition F between a C3 component and a C4 component, the latter corresponding to the decomposition of a labile pool of savannah-derived soil carbon (C SL). The mean residence time of CSL was 4.6 years. This further allowed us to partition the savannah-derived soil carbon into a labile and a stable (C SS) carbon pool. C SL accounted for 30% of soil carbon in the top soil of the savannah (0–5 cm), and only 12% when the entire 0–45 cm soil layer was considered. The decrease in C SL with time after plantation was more than compensated by an increase in Eucalyptus-derived carbon, and half of the newly incorporated Eucalyptus-derived carbon in the top soil was associated with the clay and fine silt fractions in the 14-year-old. stand. Increment in soil carbon after afforestation of tropical savannah with Eucalyptus is therefore expected despite a rapid disappearance of the labile savannah-derived carbon because a large fraction of savannah-derived carbon is stable.