Background: Given the multitude of scenarios on the future of our energy systems, multi-criteria assessments are increasingly called for to analyze and anticipate long-term effects of possible pathways with regards to their environmental, economic and social sustainability. While economic and ecologic indicators are covered through energy systems modelling and life cycle sustainability assessments, approaches to the social sustainability of future energy systems remain methodologically under-developed. Previous studies have either focused only on the social acceptance of single energy technologies or used expert-based environmental and economic indicators with social implications. Approach and results: We argue that in order to gather empirical insights on the social sustainability of future energy systems and to integrate it in multi-criteria assessments, citizens’ preferences and values need to be more systematically analyzed while informing their decisions more transparently with full life cycle data. Given the lack of theoretical underpinnings of sustainability and of empirical insights into citizens’ perceptions of sustainability with respect to future energy systems, we further argue that an explorative research design is needed. Therefore, next to six focus groups, we conducted a discrete choice experiment. The method is currently becoming more popular to analyze individuals’ preference structures for energy technologies or investments. As we show in our paper, it can be fruitfully applied to study the values and trade-offs of citizens with regards to sustainability issues. Our combined empirical methods provide two main insights with strong implications for the future development and assessment of energy pathways: While environmental and climate-related effects significantly influenced citizens’ preferences for or against certain energy pathways, total systems and production costs were of far less importance to citizens than the public discourse suggests. Conclusions: Our findings are contrary to the focus of many scenario studies that seek to optimize pathways according to total systems costs. The role of fairness and distributional justice in transition processes featured as a dominant theme in all focus groups. This adds central dimensions for future multi-criteria assessments that, so far, have been neglected by current energy systems models.