ABSTRACT It is widely recognized that the input of organic matter in tropical agriculture is essential to maintain productivity and soil quality. This study aimed to investigate the dynamics of organic C pools and CO2 emission influenced by organic compost fertilization and leucaena biomass in an area of 6 years under organic farming. The system consisted of 5 treatments based on 5 levels of fertilization with organic compost (0, 10, 20, 30, and 40 t ha−1). Each block was surrounded by leucaena and their pruning’s were distributed in equal proportions for all treatments. Two rotating crops were performed per year, cabbage/corn. Soil samples were collected in the 0–10 and 10–20 cm layers in 2-year seasons. TOC and N stocks were between 23.1 and 51.6 t ha−1, and 2.1 and 5.4 t ha−1, respectively. The highest compost doses increased the microbial biomass C and N. The increase in microbial biomass was followed by higher emissions of C-CO2. Increased microbial quotient values indicated C accumulation in the system by a higher amount of active metabolic C. The microbial biomass was less efficient in the use of the high organic compost doses. The dose of compost should be reduced and applied constantly by the farmers to attend the plant demand by nutrients and increase the efficiency of C sequestration in the soil. This C sequestration will also improve biological activity and soil quality in tropical regions, increasing food production.