The present study addresses the short-term effects of different harvest intensities under close-to-nature selective management on the upper soil layers in Slovenian and Bosnian Dinaric karst fir-beech forests. The different harvest intensities coincided with the single-tree and irregular shelterwood management, common in the region. The effect of harvesting intensity on the upper soil layers (Ol, Of, Ol and 0–10 cm mineral soil) was investigated by a repeated measurements experiment in Slovenia on 27 research plots in close-to nature managed forests. The properties of the upper layers (concentration of SOC and TN, C/N ratio, weights, BD and SOC stocks) were analyzed twice, before (2011) and after (2014) treatment of 50% and 100% harvest intensity in relation to the total standing growing stock of trees. As a control, we used no-treatment <20% harvesting intensity plots. To extend this experiment, we added three comparable plots from the Bosnian site: one in an old-growth forest with 0% harvest intensity and two in the managed forest with <20% harvest intensity. The results of the assessment of mean differences indicated a significant influence of harvesting intensity on the decrease in SOC, TN concentrations, weights and SOC stocks in the organic layers and the increase in BD and SOC stocks in the 0–10 cm mineral soil. The highest relative decreases in Ol, Of and Oh SOC stocks occurred in 50% (−10 and −38%) and 100% (−16 and −49%) harvest intensities. Negligible relative differences in both organic and 0–10 cm mineral layers were found for the <20% harvest intensity in the region. The change in forest light conditions resulting from differences in canopy openness as a function of applied harvest intensity explained the significant difference in the properties of the upper soil layers. The impact of the short-term losses in SOC stocks, in terms of overall soil productivity, may depend on the regeneration dynamics and melioration methods.