In thinning operations in Mediterranean beech forests, pack animals are often used when topographic conditions do not allow for the use of mechanisation to perform logging operations. Otherwise, mechanised extraction is the primary choice. In an effort to reduce soil disturbance caused by mechanised ground-based logging, the forest authorities who guard protected areas have been mandating animal logging at all logging sites in recent years. Since no comparative scientific trials of soil disturbance of these two extraction systems have ever been conducted in the target setting, there is no scientific evidence to sustain this approach. On this basis, we chose two study areas where the forest authorities mandated animal logging. Each study area consists of three sub-compartments, one unharvested, one harvested by animals, and one harvested by tractor in the same year (2021). We examined soil compaction, soil organic matter, and soil microarthropod biodiversity in animal skid trails, tractor skid trails, soil unaffected by extraction methods, and unharvested control sites in each study areas. We used linear mixed-effects models, indicating the study area as random intercept, to investigate the effect of the experimental treatments on the target soil features, and to check the relationship among soil physico-chemical parameters and soil microarthropod biodiversity. We discovered that only the animal and tractor skid trails showed signs of disturbance in terms of soil compaction and organic matter loss. Additionally, there was a significant decline in the biodiversity of soil microarthropods in both the skid trail types, with values of the QBS-ar index which were practically halved in comparison to the control area. We did not find any significant difference in the values in the tractor and animal skid trails for any of the examined soil characteristics. Low soil microarthropod biodiversity was found to be correlated with high soil compaction in terms of penetration resistance and low soil organic matter levels, according to linear mixed-effects models. Despite our preliminary findings, we made it clear that the short wood system by a tractor fitted with forwarding bins is unquestionably a very soil-disturbing extraction system, that ought to be avoided when conducting logging operations in protected areas. However, pack animals are not a suitable solution to reduce soil disturbance. Other extraction systems such as chute, small-scale cable yarders, as well as combination of animals and machine avoiding extensive traffic on the forest soil, are better solutions to the fundamental issue of low-impact logging in protected areas.