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Scots pine (Pinus sylvestris L.) forests are one of the main vegetation types in the Asian forest-steppe zone. However, over-harvesting currently threatens the natural regeneration and sustainability of these forests. In this study, we examine the long-term effects of different logging intensities on soil properties and natural regeneration in a natural Scots pine forest in the West Khentii Mountains (Mongolia), 19 years after selective logging. Our experimental design included five treatments: clear cut (CC), treatments with high (HI), medium (MI), low (LI) intensities, and a reference parcel with no logging impact at all (RE). We described and quantified the harvest events and applied ANOVA and LMM modeling to analyze and explain the long-term impacts of the logging intensities on soil properties and natural regeneration. We found that logging has a significant negative influence on the physical and chemical properties of the soil because it increases soil compaction and reduces soil nutrients. The most critical impacts of logging were on soil bulk density, total porosity, organic matter, and total nitrogen and phosphorus. The LMM modeling showed that organic matter (OgM), total nitrogen (TN), available K (AK) and pH values are especially impacted by logging. Our study revealed that the values for all of these variables show a linear decrease with increasing selective logging intensity and have a level of significance of p < 0.05. Another finding of this study is that selective logging with low and medium intensities can promote natural regeneration of Scots pine to numbers above those of the reference site (RE). High intensity logging and clear-cuts, however, limit the regeneration of Scots pine, reduce overall seedling numbers (p < 0.05), and create conditions that are suitable only for the regeneration of deciduous tree species. This underlines the risk of Scots pine forest degradation, either by replacement by broad-leaf trees or by conversion into non-forest ecosystems.