Fast-growing plantations are increasingly being established on tropical soils, where fertility is largely supported by soil organic matter (SOM) and where different management options of harvest organic residues is thought to impact the long-term sustainability of these plantations. The objectives of this study were: (1) to quantify the effect of contrasting methods of organic residue management on tree growth and soil CO2 effluxes in the first 2 years after planting and (2) to evaluate the impact of organic residue manipulations on the mineralization of soil organic matter over the length of the experiment. Three treatments were setup in 0.125 ha plots and replicated in three blocks at the harvesting of a Congolese Eucalyptus stand, resulting in an aboveground organic residue mass ranging from 0 to 6.3 kg m−2. The mineralization of SOM was deduced in each treatment by partitioning sources of soil CO2 effluxes using decomposition experiments and by upscaling specific root respiration. Soil CO2 effluxes were greatly affected by seasons and organic residue manipulation, although there were no significant changes in topsoil water content and topsoil temperature over most of the study period. Aboveground organic residue was the first contributor to soil CO2 efflux in the two treatments with a litter layer. Organic residue management did not significantly influence the mineralization of SOM in our study, probably due to the low quality of Eucalyptus litter, or to the hypothetical lack of dissolved organic carbon transfers from litter to soil. A strong relationship was found between cumulative heterotrophic CO2 efflux and tree growth, supporting the hypothesis that the early growth of Eucalyptus trees in a sandy tropical soil is largely dependent on the nutrients released by the decomposition of organic residues.