Given continued selective timber harvests from >500 million ha of tropical forest, forest managers need to know about its short and long-term avoidable and unavoidable consequences. Here we focus on long-term ecological impacts from an unavoidable disturbance, the soil and vegetation damage on skid trails used for log extraction. We studied recovery of main skid trails in the Australian Wet Tropics 56-years after 86 m3/ha (18 trees/ha) were harvested with bulldozers. Due to use of what are now known as reduced-impact logging practices, the main skid trails covered only 3.9% of the surface area and were mostly on ridge tops. Soil bulk density fully recovered since logging, and small-statured vegetation was denser and vertebrates more common on skid trails than in adjacent forest. Most animal activity on skid trails was by feral pigs (Sus scrofa), where predatory beetles were also scarcer and less diverse than in adjacent forest. The most prominent logging legacy was the absence of trees >20 cm diameter at breast height (DBH) on main skid trails, with basal areas half those of adjacent forest. Skid trails commonly supported ferns and sedges, and saplings that declined in density with skid traffic intensity, but there were no pioneers, invasive plants, lianas, or terrestrial bryophytes. Terrestrial LiDAR scans confirmed slow recovery of upper-story vegetation and higher mid- and lower-story densities on skid trails. Given the permanence of main skid trails, emphasis is needed on their planning, use, and closure to maximise the conservation contributions from managed tropical forests.