Mechanical site preparation (MSP) causes a mixing disturbance of the soil, which may increase decomposition of soil organic matter and subsequent carbon (C) dioxide emissions to the atmosphere. MSP also promotes the establishment and growth of tree seedlings, and hence ecosystem C fixation. However, there are uncertainties regarding net effects of MSP on C stocks at the ecosystem scale. To assess decennial effects of MSP on ecosystem C stocks, C stocks in soil, ground vegetation and trees at three experimental forest sites with Pinus contorta, Pinus sylvestris and Picea abies in Sweden were sampled and measured ca. 25 years in a control and after three MSP treatments: disc trenching, mounding and ploughing. After 25 years, all of the MSP treatments resulted in larger ecosystem C stocks than the control treatment due to positive effects on the tree biomass C stock. The tree C stock was highest after ploughing, intermediate after mounding or disc trenching, and lowest in untreated control plots at all experimental sites. The MSP treatments did not affect the soil C stocks down to 30 cm. We recommend mounding or disc trenching to promote C sequestration as they disturb sites’ ecological, aesthetic and recreational values less than ploughing.