The northern boreal forests in Fennoscandia have been managed for decades using clear-cut harvesting and subsequent mechanical site preparation (MSP). MSP is intended to reduce competing vegetation, improve soil temperature and water conditions as well as mobilize nutrients for the use by outplanted seedlings. The use of heavy machinery, particularly bulldozer-driven Marttiini-plough, has raised concerns about soil quality and therefore sustainability of forest productivity and forest floor diversity. We applied soil physical measurements and inventories of naturally established Norway spruce (Picea abies (L.) Karst.) to investigate these concerns 16–18 years after intensive forest management in Finnish Lapland. MSP with Marttiini-plough had inverted Podzol soil profile and created the following micro-sites: trench, tilt and untreated (UTR) soil between the ploughed tracks at former spruce sites. The soil electrical conductivity (ECa) and soil solution conductivity (ECw) at micro-sites of spruce seedling/saplings, differed significantly (p ECwTILT = 10.7 ± 9.2mSm−1 > ECwTRENCH = 2.2 ± 2.9mSm−1. Spruce individuals at UTR (mean height 127 ± 89 cm) and tilt (111 ± 74 cm) were significantly (p < 0.001) taller compared to those in trench (32 ± 44 cm). The five study sites were surrounded by mature Norway spruce stands, yet only 0–14% of spruce seedlings/saplings were found on the MSP-exposed mineral soil. These results imply that intensive forest practices result in losses in soil nutrient supply, hence endangering sustainability of the soil quality, and therefore occasionally hamper natural regeneration of Norway spruce.