The 2015 Paris Agreement encourages stakeholders to implement sustainable forest management policies to mitigate anthropogenic emissions of greenhouse gases (GHG). The net effects of forest management on the climate and the environment are, however, still not completely understood, partially as a result of a lack of long-term measurements of GHG fluxes in managed forests. During the period 2010–2013, we simultaneously measured carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) fluxes using the flux-gradient technique at two clear-cut plots of different degrees of wetness, located in central Sweden. The measurements started approx. one year after clear-cutting, directly following soil scarification and planting. The study focused on robust inter-plot comparisons, spatial and temporal dynamics of GHG fluxes, and the determination of the global warming potential of a clear-cut boreal forest. The clear-cutting resulted in significant emissions of GHGs at both the wet and the dry plot. The degree of wetness determined, directly or indirectly, the relative contribution of each GHG to the total budgets. Faster establishment of vegetation on the wet plot reduced total emissions of CO2 as compared to the dry plot but this was partially offset by higher CH4 emissions. Waterlogging following clear-cutting likely caused both plots to switch from sinks to sources of CH4. In addition, there were periods with N2O uptake at the wet plot, although both plots were net sources of N2O on an annual basis. We observed clear diel patters in CO2, CH4 and N2O fluxes during the growing season at both plots, with the exception of CH4 at the dry plot. The total three-year carbon budgets were 4107 gCO2-equivalent m−2 and 5274 gCO2-equivalent m−2 at the wet and the dry plots, respectively. CO2 contributed 91.8% to the total carbon budget at the wet plot and 98.2% at the dry plot. For the only full year with N2O measurements, the total GHG budgets were 1069.9 gCO2-eqvivalents m−2 and 1695.7 gCO2-eqvivalents m−2 at the wet and dry plot, respectively. At the wet plot, CH4 contributed 3.7%, while N2O contributed 7.3%. At the dry plot, CH4 and N2O contributed 1.5% and 7.6%, respectively. Our results emphasize the importance of considering the effects of the three GHGs on the climate for any forest management policy aiming at enhancing the mitigation potential of forests.