In intensively managed forest plantations, clear-cutting and intensive site preparation may have negative effects on fundamental soil processes that determine the sustainability of these systems. This study was conducted to evaluate the effects of highly mechanized site preparation—involving the removal of organic residues (humus layer and slash)—on soil properties and tree growth in radiata pine plantations growing on steep forest land in northern Spain. In spite of the high risk of erosion, this type of management is carried out without any consideration for soil conservation. These plantations are growing on acidic soils with low reserves of available nutrients and therefore nutrient deficiencies may occur in the medium or long term. Site preparation caused moderate to considerable soil compaction and the effects were still pronounced after 9 years. As a consequence of accelerated erosion and soil disturbance, significant depletion of soil organic matter, Ca and Mg available nutrients, cation exchange capacity and base saturation were observed after removal of logging residues; in the most severe cases the effects were still detected 9 years after site preparation. Availability of Ca to trees was also reduced. Nine years after site preparation, scalped and ploughed soils also showed decreased microbial biomass, lower microbial activity, and less aerobic and anaerobic mineralizable N. Tree growth was significantly reduced where the logging residues and humus layer were removed, especially when this was followed by deep ploughing. During the 9 years of the study, the mean annual increment of timber volume decreased from 8.4 to 2.4 m 3 ha −1. We conclude that leaving logging residues on site avoids soil compaction, favours nutrient uptake in trees and maintains soil biological properties. On the basis of these results, the retention of logging residues and reduction of soil perturbation during site preparation are highly recommended.