Climatic parameters (temperature and precipitation) and vegetation are the main factors controlling C dynamics in tropical forests. While climatic parameters have received attention, there is not enough data on how vegetation type contributes to the overall C balance. The objective of this study was to assess the relationship between soil properties and CO2 emissions among individual plant species. Soil CO2 emissions were measured along plant species in a primary forest and a fallow at Masako Forest Reserve, Kisangani, Democratic Republic of Congo, using an infra-red Vernier CO2 Gas Sensor. The Vernier sensor was inserted into a plastic chamber 25 cm long and 15 cm in diameter, connected to a lab-quest interface and a laptop. Vernier’s CO2 measurements were calibrated with a Vaisala soil CO2 chamber. Soil temperature (T) and volumetric water content (θv) were directly measured in the 0–10 cm layer with Decagon sensors. The plants studied were local species. In both fallow and primary forests, θv, T and CO2 were significantly affected by plant species (p = 0.0001). CO2 emissions ranged from 323.37 to 388.71 ug C–CO2 m2h−1 in the fallow and 224.88 to 377.93 ug C–CO2 m2h−1 in the primary forest. Soil grown to Elaeis guineensis and Gilbertiodendron dewervrei had the highest CO2 emissions in the fallow and primary forests, respectively. θv was highest in Ananas comosus in the fallow and Picnatus angolensis grown soils in the primary forest. The highest T was recorded in soil grown to Nephrolepis biserrata in the fallow, while the lowest T was in Gilbertiodendron dewervrei occupied soil in the primary forest. Overall, the fallow soil had more water (p = 0.0001), higher temperature (p = 0.0001), and consequently higher CO2 emissions (p = 0.0001). Correlation analysis between climatic factors (T and θv) and CO2 emissions showed significant positive or negative trends, depending on plant species. In the context of climate change, the results suggest that primary forest will be a more efficient carbon sink than forest fallow. This study will be repeated for a second year to understand better the dynamics of CO2 emissions and soil-controlling factors at Masako Forest Reserve.