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Forest harvest residues are important raw materials for bioenergy in regions practicing forestry. Removing these residues from a harvest site reduces the carbon stock of the forest compared with conventional stem-only harvest because less litter in left on the site. The indirect carbon dioxide (CO2) emission from producing bioenergy occur when carbon in the logging residues is emitted into the atmosphere at once through combustion, instead of being released little by little as a result of decomposition at the harvest sites. In this study (1) we introduce an approach to calculate this indirect emission from using logging residues for bioenergy production, and (2) estimate this emission at a typical target of harvest residue removal, i.e. boreal Norway spruce forest in Finland. The removal of stumps caused a larger indirect emission per unit of energy produced than the removal of branches because of a lower decomposition rate of the stumps. The indirect emission per unit of energy produced decreased with time since starting to collect the harvest residues as a result of decomposition at older harvest sites. During the 100 years of conducting this practice, the indirect emission from average-sized branches (diameter 2 cm) decreased from 340 to 70 kg CO2 eq. MWh−1 and that from stumps (diameter 26 cm) from 340 to 160 kg CO2 eq. MWh−1. These emissions are an order of magnitude larger than the other emissions (collecting, transporting, etc.) from the bioenergy production chain. When the bioenergy production was started, the total emissions were comparable to fossil fuels. The practice had to be carried out for 22 (stumps) or four (branches) years until the total emissions dropped below the emissions of natural gas. Our results emphasize the importance of accounting for land-use-related indirect emissions to correctly estimate the efficiency of bioenergy in reducing CO2 emission into the atmosphere.