The recovery of soil properties and the proper growth of natural tree regeneration are key elements for maintaining forest productivity after selective logging operations. This study was conducted on the soil properties and natural growth of two pioneer seedling species of alder and maple which were on skid trails in the mixed beech forests of northern Iran. To examine the long-term effects, we randomly selected six skid trails, with two replicates established for each of three time periods since last use (10, 20, and 30 years ago). Random plots 4 m × 10 m in size, three plots on each skid trail and six plots on areas without soil compaction (control), were selected. Measurements included the physical and chemical properties of the soil and the growth, and the architectural and qualitative characteristics of the seedlings. The results showed that all the soil properties of the 10- and 20-year-old skid trails were significantly different from the control area (except for the soil moisture in the 20-year-old skid trail). The 30-year-old skid trail showed values of other soil properties which were not significantly different from the control area, except for the amounts of organic matter and soil nitrogen, which was less than the control. The skid trails had a negative effect on all of the growth, qualitative, and architectural indices of seedlings. The characteristics of seedlings were related to soil characteristics and had the highest correlation with the soil penetration resistance (R-value from -0.41 to -0.63 for stem growth, p < 0.05; -0.57 to -0.90 for root growth, p < 0.01; and -0.76 to -0.86 for biomass, p < 0.01). The correlation coefficient between soil penetration resistance and the Dickson quality index of alder and maple seedlings was, respectively, -0.74 and -0.72, p < 0.01. The negative effect of soil compaction on root growth (-27.69% for alder seedlings and -28.08% for maple seedlings) was greater than on stem growth (-24.11% for alder seedlings and -16.27% for maple seedlings). The amount of growth, qualitative, and architectural indices of alder seedlings were higher than that of maple seedlings. Although alder is a better choice as compared to maple seedling in the initial year, the results of our study show that it is recommended to plant both alder and maple on skid trails after logging operations.