Boreal forest soils store more carbon than the aboveground vegetation and play a critical role in the global carbon cycle and ecosystem function. Despite their importance, the long-term impacts of forest management on soil organic carbon (SOC) remain unclear, especially in boreal forests with contrasting climatic conditions. This study assesses the effects of commercial thinning on SOC stocks (20-year post-treatment) in black spruce stands across two boreal regions in Québec: the warmer, drier Abitibi and the colder, wetter Cote-Nord, accounting also spatial variability from skidding strips. We measured SOC stocks at three soil depths (forest floor, mineral layer: 0–15 and 15–30 cm) in both thinned and unmanaged stands, using bulk density and SOC concentration. Soil pH, cation exchange capacity (CEC), and macronutrients were also conducted to characterize soil fertility. Thinning had no effect on total SOC stocks of the whole profile in either region, but horizon-specific differences were detected. A decrease in forest floor SOC stocks was observed in Côte-Nord, whereas SOC stocks in Abitibi remained similar. These contrasting outcomes reflect regional differences in soil fertility (higher CEC, potassium in Abitibi) and climatic conditions which may have influenced vegetation regrowth and, consequently, SOC stocks’ recovery over time. Although SOC stocks decreased in skidding strips, their small proportion within the stand minimized their effect on total SOC stocks at the plot level. Overall, the study emphasizes the need to consider climatic and soil context, as well as limited spatial extent of skidding strips, in evaluating silvicultural impacts on boreal carbon sequestration.