The majority of European forests are managed and influenced by natural disturbances, with wind being the dominant agent, both of which affect the ecosystem's carbon budget. Therefore, investigating the combined effect of wind damage and different soil preparation practices on forest carbon pools is of great importance. This study examines changes in carbon stocks in the soil and biomass of two 5-year-old Scots pine stands (namely Tlen1 and Tlen2), which were established approximately 2 years after a large-scale wind disturbance in northwestern Poland. These neighboring sites differ in terms of the reforestation methods applied, particularly regarding soil preparation: ploughing disc trenching at Tlen1 and partial preparation through local manual scalping at Tlen2. Using nearby forest soils as the best available reference for the pre-windthrow state, it was estimated that the total carbon stock in the soil (up to 50 cm depth, both organic and mineral) was depleted by approximately 17 % at Tlen1 and 7 % at Tlen2. The between-site differences were around 18 %, which nearly doubled when considering only the top 20 cm of the soil profile. In contrast, the total biomass, as well as the carbon stock in biomass, were significantly higher at the site with soil prepared using moderate ploughing (Tlen1) compared to the area with partial soil preparation (Tlen2). Our findings indicate that ploughing disc trenching, aimed mainly at weed removal and improving soil properties, significantly enhanced Scots pine seedlings' growth, survival, and development during the first four years after planting. Finally, when both carbon stock estimates are pooled together, regardless of the chosen technique, the growing biomass in the investigated stands did not fully compensate for the carbon losses caused by mechanical soil preparation. However, in the short term, the overall change in the ecosystem's carbon balance was only slightly negative and comparable between the two sites.