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Ditch cleaning (DC) is increasingly applied to facilitate forest regeneration following clear-cutting in Fennoscandinavia. However, its impact on the ecosystem carbon and greenhouse gas (GHG) balances is poorly understood. We conducted chamber measurements to assess the initial DC effects on carbon dioxide (CO2) and methane (CH4) fluxes in a recent forest clear-cut on wet mineral soil in boreal Sweden. Measurements were conducted in two adjacent areas over two pre-treatments (2018/19) and two years (2020/21) after conducting DC in one area. We further assessed the spatial variation of fluxes at three distances (4, 20, 40 m) from ditches. We found that DC lowered the water table level by 12 ± 2 cm (mean ± standard error) and topsoil moisture by 0.12 ± 0.01 m3 m−3. DC had a limited initial effect on the net CO2 exchange and its component fluxes. CH4 emissions were low during the dry pre-treatment years but increased particularly in the control area during the wet years of 2020/21. Distance to ditch had no consistent effects on CO2 and CH4 fluxes. Model extrapolations suggest that annual carbon emissions decreased over the four years from 6.7 ± 1.4 to 1.6 ± 1.6 t-C ha−1 year−1, without treatment differences. Annual CH4 emissions contributed