The aim of this paper is to present a decision support system (DSS) to capture the complexity of the transition of a national energy system to net zero in the context of multiple sustainability themes. The paper proposes an integrated assessment framework that combines dynamic systems modeling, sustainability indicators, and multi-criteria decision analysis (MCDA) with direct stakeholder involvement. To illustrate the use of the DSS, the paper compares bundles of climate change policies that aim to decarbonize the road transport sector in Iceland. Eighteen scenarios and alternative development trajectories are defined for the Icelandic energy system based on a combination of three main driving forces. These are, firstly, economic development (three cases); secondly, changes in energy efficiency (two cases); and finally, three climate policy bundles aimed at increasing the share of electric vehicles. Based on the results from the integrated assessment framework, the performance scores of the climate policy bundles are compared across the following five sustainability themes: social impact; economic development; environmental impact; energy security; and technical aspects. The findings confirm that a different conclusion may be reached when multiple sustainability themes are applied in the selection of preferred policy bundles as compared to conventional techno-economic criteria. Banning the registration of fossil-fueled vehicles, combined with economic instruments, offers the best decarbonizing strategy to reach climate and energy policy goals simultaneously.