Organic-rich agricultural soils, including drained peatlands, are hotspots for biogenic CO2 emissions. Due to microbial mineralisation, the organic carbon (OC) content of these soils transitions to that of mineral soils, but it remains unclear how the residual OC content controls the rate of CO2 emission. Here we show that area-scaled CO2 emissions from topsoils with >6% OC are not controlled by OC content and OC density in a comprehensive laboratory incubation experiment. National greenhouse gas inventories assign area-scaled CO2 emission factors to soils with >12% OC, while soils with 6-12% OC are mostly disregarded or treated with lower emission factors. In this respect, our results suggest that CO2 emissions from organic soils could be underestimated by up to 40% in the Danish national inventory submission to the United Nations Framework Convention on Climate Change (UNFCCC). We conclude that global underestimation of area-scaled CO2 emissions from 6-12% OC soils occurs in countries with large proportions of organic soils in transition from organic to organo-mineral soils due to agricultural management. Refining CO2 emission estimates for 6-12% OC soils is critical for the accuracy of national inventories, but also for recognising the climate benefits of initiatives to rewet drained organic soils.