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Central European forestry has started an ecologically-oriented conversion of spruce monocultures to broadleaf and mixed forests. Spruce stands in the mountains of south Poland are replaced mainly by beech. However, there is limited knowledge about the effects of “native” forest reconstruction on soil organic carbon (SOC) pools on a regional scale. We approximated the present SOC stocks and probable total SOC losses based on an inventory conducted on 373 monitoring plots in the Stolowe Mountains National Park, SW Poland, where Norway spruce prevails in 83% of forest stands. SOC pools are in relation to an altitude, soil and bedrock type; however, on all soils SOC are the lowest in pure beech stands. SOC pools in the forest litter under spruce monocultures are twofold larger than under beech. Mean present-day SOC stocks are 202 and 152 Mg ha− 1 (0–100 cm mineral soil + forest litter), respectively under spruce and beech. However, this 25%-difference in mean soil carbon stock between pure spruce and beech stands does not define the real SOC losses followed species replacement on a regional scale. When taking into account the present and target forest structures (evaluated in relation to soil quality, local climate and land morphology) an approximated long-term regional decrease of SOC stock is no larger than 7% in a 100 cm-thick soil profile or 10% in upper 20 cm layer.