A shift in management to improve the ecological function of mature plantations of exotic species can have important effects on the ecosystem climate mitigation potential. This study investigated the effect of two common forest management strategies for Scots pine (Pinus sylvestris L.) stands on the C storage after 15 years of management. Two pairs of forest stands on poor sandy soil and under the maritime influence in Brasschaat, Belgium, were observed as case studies. The observed forest management strategies were (i) thinning and group planting of oak saplings (Quercus robur L.) and (ii) clear cut, followed by replanting of young oak. For each stand, all forest C pools (aboveground biomass, belowground biomass, litter, and mineral soil) were determined. Results showed, surprisingly, no significant difference in the whole ecosystem C stock for both forest management strategies after 15 years of management. However, after the clear cut and the new plantation, the C in the top 30 cm layer of the mineral soil increased, while it decreased on the forest floor. For thinning with group planting, the C stocks reduced within the 10–30 cm soil layer without impact on the total soil C. Therefore, the shift in management did result in a different allocation of the belowground C, particularly after a clear cut. The results are not only relevant for the study region but also for managed Scots pine forests in neighboring regions of the Atlantic zone of Western Europe.