Sustainable forest management plays a key role for forest biodiversity and the provisioning of ecosystem services (BES), including the important service of carbon sequestration for climate change mitigation. Forest managers, however, find themselves in the increasingly complex planning situation to balance the often conflicting demands in BES. To cope with this situation, a prototype of a decision support system (DSS) for strategic (long-term) planning at the forest enterprise level was developed in the present project. The DSS was applied at three case study enterprises (CSEs) in Northern Switzerland, two lowland and one higher-elevation enterprise, for a 50-year time horizon (2010 to 2060) under present climate and three climate change scenarios (‘wet’, ‘medium’, ‘dry’). BES provisioning (for biodiversity, timber production, recreation, protection against gravitational hazards and carbon sequestration) was evaluated for four management scenarios (no management, current (BAU), lower and higher management intensity) using a utility-based multi-criteria decision analysis. Additionally, four alternative preference scenarios for BES provisioning were investigated to evaluate the robustness of the results to shifting BES preferences. At all CSEs, synergies between carbon sequestration, biodiversity and protection function as well as trade-offs between carbon sequestration and timber production occurred. The BAU management resulted in the highest overall utility in 2060 for different climate and BES preference scenarios, with the exception of one lowland CSE under current BES preference, where a lower intensity management performed best. Although climate change had a relatively small effect on overall utility, individual BES indicators showed a negative climate change impact for the lowland CSEs and a positive effect for the higher elevation CSE. The patterns of overall utility were relatively stable to shifts in BES preferences, with exception of a shift toward a preference for carbon sequestration. Overall, the study demonstrates the potential of the DSS to investigate the development of multiple BES as well as their synergies and trade-offs for a set of lowland and mountainous forest enterprises. The new system incorporates a wide set of BES indicators, a strong empirical foundation and a flexible multi-criteria decision analysis, enabling stakeholders to take scientifically well-founded decisions under changing climatic conditions and political goals.