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The agricultural use of organic soils usually requires drainage, resulting in soil subsidence and high greenhouse gas (GHG) emissions, mainly CO2. One proposed strategy to maintain the productivity of these soils is adding a mineral soil cover. However, its impact on the GHG budget has yet to be discovered. Herein, we determined the net ecosystem carbon budget (NECB) for a pair of covered (Cov) and uncovered (reference, Ref) organic soils under intensive grassland management in the Rhine Valley, Switzerland, over four years (1 March 2018–29 February 2022). The net ecosystem exchange (NEE) of CO2 fluxes was measured using the eddy covariance method, in addition to recording additional carbon exports and imports for harvest and organic fertilisers. N2O and CH4 fluxes were measured using an automatic time-integrating chamber system over three years. Both of the drained peatlands under agricultural use showed substantial soil organic carbon (SOC) losses of 175 to 786 g Cm- 2 year -1 (Ref) and 125 to 826 g C m- 2 year -1 (Cov). The annual losses were driven by the aerated peat carbon stock during summer and accounted for 0.5 – 1.4 % of it. Covering the organic soil with a mineral layer did not significantly reduce the SOC losses relative to the reference site in any of the four years, and CH4 uptake was marginal. However, soil coverage significantly reduced the three-year average N2O emissions from 1.5 (Ref) to 0.2 g N m-2 year-1 (Cov) and consequently the net GHG budget from 19.2±2.0 to 12.8±2.1 t CO2 eq. ha- 1year-1. We conclude that mineral soil coverage per se has little potential to reduce carbon losses from drained organic soils. However, if combined with a considerable rise in the water table, SOC losses may be effectively reduced while maintaining agricultural productivity.