This study investigated the C mineralization and chemical modification of a typical tropical soil amended with regional compost of different stability. Compost samples were produced from coffee pulp and fruit and vegetable waste in a method of small heap composting and the samples were collected in three different phases of composting. Both the fresh waste and compost samples were analyzed for their phytotoxicity. These samples were added to a tropical Nitisol at the rate of 48 t ha?1 and a control was set up without amendment. The CO2-C respired was determined during 98 days of incubation and the incubated samples were taken at the start and end of incubation for molecular-chemical analysis by Pyrolysis-Field Ionization Mass Spectrometry (Py-FIMS). The fresh waste yielded a germination index (GI) < 26% indicating phytotoxicity but this disappeared in all the composts (GI > 100%). The CO2-C respired was best explained by a first order plus linear model. A soil amended with a compost taken at the thermophilic phase attained the lowest overall organic C loss. In general, the Py-FIMS revealed a significant enrichment of stable N-compounds during the incubation in all amended soils compared to the control. Furthermore, among the compost-soil mixtures Py-FIMS indicated significantly higher increases in the proportions of carbohydrates, peptides and phenols/lignin monomers at the expense of fatty acids and sterols in soil amended with composts from the thermophilic phase. Thermal volatilization curves of Py-FIMS indicated enrichments of stable N-compounds and peptides in compost amended soil. This was a result of enhanced decomposition and stabilization of decomposition products by physical protection through association with clay and soil aggregates. In summary, application of compost shortly after reaching the high temperature phase was shown to be more efficient in organic C sequestration in a clay-rich tropical agricultural soil than mature composts.