The demand and potential for increasing the use of bioenergy from harvest residues in Sweden are large. However, harvest residue (branches and tops) and stump extraction negatively affect soil organic carbon (SOC) accumulation. The main objective of this study was to assess the effects of increased harvest residue extraction on soil organic carbon (SOC) accumulation at national level. Further, the reduction in CO2 by substituting coal with biofuel from harvest residues and stumps was assessed. Several scenarios with increased harvest residue extraction were simulated with the forest management system HUGIN and the SOC decomposition model Q and the effects on SOC accumulation in Swedish coniferous forest soils were assessed. All scenarios resulted in decreased SOC accumulation. The decrease in SOC accumulation was largest for stump extraction, with 0.15 Mg C ha(-1) y(-1) loss on average over a 100-year simulation period. In all scenarios, the short-term effects on SOC accumulation were greater than the long-term effects. The effect of substituting coal with bioenergy was an immediate reduction of net CO2 emissions. An increase in the use of forest residues leads to CO2 mitigation in the atmosphere, even when SOC losses are accounted for. (C) 2014 Elsevier Ltd. All rights reserved.