We studied in central Finland whether stump harvesting after clear felling of coniferous forest poses further short-term changes in soil carbon and nitrogen dynamics when compared to the traditional site preparation method, mounding. Exposed mineral soil patches in Norway spruce (Picea abies) dominated clear-cut stands were sampled 1–5 years after the treatments. The extent of the exposed mineral soil surface was significantly larger at the stump removal sites when compared to the mounding sites. No differences were found in soil pH, organic matter content or total concentration of soil C between the treatments or treatment years. Total concentration of soil N was consistently higher and C:N ratio lower in the stump removal plots than in the mounded plots. Further, both net N mineralisation and nitrification were clearly increased in the stump removal plots one year after the treatments. Soil microbial activity (CO2 production) was higher in the stump removal plots but similar difference was not found in sieved soil samples incubated in the laboratory. Fluxes of other important greenhouse gases (CH4 and N2O) did not seem to be affected by stump removal. The differences between the stump removal and mounding procedures were most obviously attributed to more substantial soil disturbance by stump pulling and/or differences in the microbial communities and quality of soil organic matter in the differently treated soil.