An important aspect of sustainable forest management is to assess the impact of forest operations on ecosystem services. This work analyzed the long-term effect of two standard thinning regimes on carbon stocks both in tree biomass and soil compartments as well as its effect on soil condition. The target population was a 90-year-old Scots pine (Pinus sylvestris L.) stand in southwestern Europe. Soil condition was measured as dry mass of the forest floor and concentration of carbon, nutrients in the forest floor as well as exchangeable cations, effective cation exchange capacity, pH and bulk density in the mineral soil. Repeated thinnings from below in a southern European population of Scots pine led to a reduction in current on-site carbon stock in tree biomass of 28% in moderately thinned stands (D grade: average residual basal area of 65–79% relative to the control plots) which was consistent with an observed loss of volume production. However, the inclusion of the amount of carbon exported off-site with harvested biomass reduced the decrease in stock to 4.8%. Nutrient concentrations in the forest floor increased in moderate thinned stands (P, K, Mg and Mn) or were unchanged (C, N and Fe). The selected thinning regime did not alter mineral soil condition. A decreasing pattern of Ca and Mn stocks with depth was consistent with a high reduction of nutrient concentration of elements and higher bulk density with depth. However K, Mg and Na showed stable stocks across depths because of a much smaller reduction of nutrient concentrations in deeper layers relative to the surface layer. We hypothesized that this stable pattern with soil depth was due to leaching. The sustainability of forest thinning is a trade-off between loss of standing biomass and increasing stand stability as long as other indicators, like soil condition, do not significantly change.