Drained peatlands are CO₂ hotspots and lose important soil functions over time. In contrast to mineral soils, their high carbon density induces long lasting and high emissions. These emissions can be estimated using various approaches which cover different system boundaries in time and space. Here we compare 5 years flux measurements from manual chambers with a soil profile based method to estimate carbon losses from two temperate fens under different management intensity drained at the end of the 19th century. According to the flux measurements, both grassland sites currently lose significant amounts of carbon as CO₂ in the order of 7.1 and 9.1 t CO₂-C ha^−1a^−1 when managed non-intensively or intensively, respectively. Profile based estimates, which make use of the difference in ash concentration along the soil profile, reveal a total of 284 and 619 t C ha^−1 since the onset of drainage. These substantial losses are accompanied by a sharp decrease in peat quality as measured by NMR spectroscopy, confirming that a large part of former topsoil material is already mineralized. On average, the profile based estimate converts to smaller annual loss rates of 2.2 (non-intensive) and 4.8 t CO₂−C ha^−1a^−1 (intensive) management. Our data, together with historical flux measurements at this site, provide evidence that peat decomposition rates increased over time, despite declining organic matter quality. We suggest that higher management intensities (i.e., higher fertilization and changes in carbon export from the field), including drainage, and increased mean annual temperature may be important factors for higher emissions today. These two methods are complementary in terms of time horizon and system boundary and, in conjunction, confirm the long-term emission potential of temperate drained organic grassland soils.