Carbon sequestered in biomass is not necessarily stored infinitely, but is exposed to human or natural disturbances. Storm is the most important natural disturbance agent in Swiss forests. Therefore, if forests are taken into account in the national carbon budget, the impact of windthrow on carbon pools and fluxes should be included. In this article the forest scenario model MASSIMO and the soil carbon model YASSO were applied to assess the effect of forest management and an increased storm activity on the carbon sequestration in Swiss forests. First, the soil model was; adapted to Swiss conditions and validated. Second, carbon fluxes were assessed applying the two models under various forest management scenarios and storm frequencies. In particular, the influence of clearing after a storm event on the carbon budget was analyzed. The evaluation of the model results showed that the soil model reliably reproduces the amount of soil carbon at the test sites. The simulation results indicated that, within the simulated time period of 40 years, forest management has a strong influence on the carbon budget. However, forest soils only react slightly to changes in the above-ground biomass. The results also showed that a storm frequency increase of 30% has a small impact on the national carbon budget of forests. To develop effective mitigation strategies for forest management, however, longer time periods must be regarded.