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One way of increasing the supply of renewable energy, thereby decreasing the use of fossil fuels, is to extract the stumps that remain after final stem harvesting. However, little is known about the environmental consequences of stump harvesting, and how ecosystem services, such as carbon sequestration, are affected by the practice. In the present paper, the effects on the soil carbon pool during the first months and years after stump harvesting in former Norway spruce stands are presented. The study was performed at two sites in mid- and southern Sweden. At both sites, the soil CO2 flux was measured on several occasions with a portable respiration system, to compare plots on which stump harvesting had occurred, with reference plots. At one of the sites, CO2 exchange was also followed continuously by means of eddy-covariance measurements before and after stump harvesting. Since there was no vegetation at the beginning of the study, almost all emitted CO2 could be assumed to come from heterotrophic sources, and the soil CO2 flux was measured. This study shows that the effect of stump harvesting on CO2 flux or soil decomposition processes is small or absent compared to site preparation such as mounding in a short-term perspective of months and years. The long-term consequences of stump harvesting are, however, still uncertain.