Carbon (C) cycling in the boreal forest is driven by both natural and human disturbances, but there is little information on the impact of forest management practices on ecosystem-level C balance. We evaluated the C balance of a recently harvested boreal site in eastern Canada by measuring CO2 fluxes with the eddy covariance technique for 1 year before the application of a scarification treatment (mechanical site preparation) and for 1 year after the treatment was applied to approximately 40% of the study area. Net annual exchange indicated a source of 111 g C m−2 year−1 before scarification that increased to 175 g C m−2 year−1 after treatment. Annual gross ecosystem productivity (GEP) and net C flux varied between years, but there was no significant difference for ecosystem respiration. Since the differences in climate between years did not explain the changes in the site C balance and daytime net C sequestration under non-limiting environmental conditions was generally lower after the treatment, the large difference in C emissions was most likely due to decreased GEP resulting from the destruction of approximately 60% of the living aboveground vegetation within the scarified areas. Although daily NEP was almost always negative throughout the year, a net daily C sink was observed during a 2-week period in late summer 2003 when air temperatures were approximately 8 °C cooler than preceding weeks. An analysis of the residuals from light–response regressions showed that soil water content and vapor pressure deficit were the second most important variables explaining morning and afternoon net C flux in 2003 and 2004, respectively.