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Forest management, especially thinning and harvesting measures, has a significant impact on the forest carbon balance especially in the forests with long-term continuous cover history. We measured soil CO2 efflux (Rs) in three forest complexes of mixed, uneven-aged Dinaric forests with predominating silver fir (Abies alba Mill.), beech (Fagus sylvatica L.), and Norway spruce (Picea abies Karst.). Rs was measured after removal of mature forest stands with 50% and 100% intensity of living stock and compared with Rs on the control plots without any applied silvicultural measures. Rs was measured monthly in three consecutive 2012, 2013 and 2014 growing periods. Soil CO2 efflux increased after harvest of both intensities in all studied forest stands. The biggest increase was measured in beech stands and amounted up to 47 and 69% for 50% and 100% harvest intensities, respectively. The effect of harvest on Rs in spruce and fir stands was similar – up to 26% for 50% harvest intensity and 48% for 100% harvest intensity. Despite the biggest increase after harvest, Rs in beech stands returned the fastest to the level of the uncut forest and this levelling period (LP) took 14–17 months with a little delay of the stands with 100% harvest intensity. The LP for all fir stands, for spruce stands with 50% harvest intensity and for one spruce stand with 100% harvest intensity, was 26–29 months. At two spruce stands with 100% harvest intensity we did not record Rs levelling during our three-year study. This study involved forest stands of three predominating tree species growing under the same conditions, which allowed us to determine the species-specific sensitivity of soil CO2 efflux to the different harvesting intensities.