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Forest soils store large stocks of soil organic matter (SOM) and are of vital importance for the ecosystem supply with nutrients and water. According to the available literature, depending on management regime and site properties, different negative and positive effects of forest management (particularly of forest thinnings and shelterwood cuttings) on soil organic carbon (SOC) and nitrogen (N) stocks are observed. To elucidate the long-term impact of different shelterwood systems and small clear-cuttings on the OC and N stocks of shallow calcareous soils in the Bavarian Alps, we conducted soil humus inventories on different plots of a mixed mountain forest management experiment started in 1976. The silvicultural multi-treatment experiment consists of a NW-exposed Main Experiment (ME) site with eight plots of different cutting intensity (two unthinned controls, two light shelterwood cuttings = 30 % of basal tree area removed, two heavy shelterwood cuttings = 50 % removed, and two clear-cuttings = 100 % removed) on Triassic dolostone. Additionally, plots were installed at a N-exposed dolostone (ND) site and two sites (FL, FH) on Flysch sandstone (each with one unthinned control and one heavy shelterwood cutting). The shelterwood cuttings from 1976 were repeated in 2003 to re-establish the overstorey basal area as produced by the first cutting in the different plots. Thirty-five years after the first treatments, forest floor SOC and N stocks were significantly decreased (up to −70 %) at the different shelterwood and clear-cut treatments compared to the unthinned control at the ME site despite vigorous development of natural rejuvenation. Also significantly smaller topsoil (forest floor plus mineral soil 0-10 cm depth) OC stocks (between −16 and −20 %) were detected at the thinned compared to the control plots. Differences in topsoil N stocks were also considerable (between −3 and −14 %), but substantially smaller than OC stock changes. For the total soil down to 30 cm depth, OC stocks in the differently thinned plots were consistently smaller compared to the unthinned control plots. Comparable to our findings at the ME site, heavy shelterwood plots at the three other sites (ND, FL, and FH) showed significant losses of OC in the forest floor (up to 43 %), mineral soil (up to 38 %), topsoil (up to 38 %), and total soil (up to 34 %). Significant large absolute and relative SOC decreases coincided with sites characterized by large initial humus stocks. Moreover, significant effects of heavy shelterwood cuttings on SOC and N stocks (on average 23 % SOC loss and 13 % soil N loss for the forest floor plus the uppermost 10 cm mineral soil) were detected on a regional level. Our results show that different shelterwood systems are accompanied with a considerable long-term decrease in OC and N stocks in shallow calcareous forest soils of the Bavarian Alps. However, a comparison with a windthrown forest stand at a nearby similar site indicates that SOM losses after thinning operations are small compared to decreases following windthrow or other calamities with subsequent large soil erosion and increased mineralization processes. [ABSTRACT FROM AUTHOR]