Post-fire salvage logging is a common silvicultural practice around the world, with the potential to alter the regenerative capacity of an ecosystem and thus its role as a source or a sink of carbon. However, there is no information on the effect of burnt wood management on the net ecosystem carbon balance. Here, we examine for the first time the effect of post-fire burnt wood management on the net ecosystem carbon balance by comparing the carbon exchange of two treatments in a burnt Mediterranean coniferous forest treated by salvage logging (SL, felling and removing the logs and masticating the woody debris) and Non-Intervention (NI, all trees left standing) using eddy covariance measurements. Using different partitioning approaches, we analyze the evolution of photosynthesis and respiration processes together with measurements of vegetation cover and soil respiration and humidity to interpret the differences in the measured fluxes and underlying processes. Results show that SL enhanced CO₂ emissions of this burnt pine forest by more than 120gCm⁻² compared to the NI treatment for the period June–December 2009. Although soil respiration was around 30% higher in NI during growing season, this was more than offset by photosynthesis, as corroborated by increases in vegetation cover and evapotranspiration. Since SL is counterproductive to climate-change and Kyoto protocol objectives of optimal C sequestration by terrestrial ecosystems, less aggressive burnt wood management policies should be considered.