The increased interest in harvesting logging residues as a source of bio-energy has led to concerns about the potentially adverse long-term impact of the practice on site productivity. The aim of this study was to examine the effects on soil chemistry (pH, C, N and AL-extractable P, K, Ca and Mg) in three different soil layers (FH, 0–5 cm and 5–10 cm mineral soil) and understorey vegetation after the second removal of logging residues in whole-tree thinned stands. The study was performed at four different sites, established in the period 1984–87, representing a range of different climatic and soil conditions: a very fertile Norway spruce (Picea abies (L.) Karst.) site in south-western Sweden and three Scots pine (Pinus sylvestris L.) sites located in south, south-central and central Sweden. The effects of whole-tree thinning on soil chemistry and understorey vegetation were generally minor and variable. Across all sites the concentrations of Ca and Mg were significantly lower when slash was removed.