The Paris Agreement is the first-ever universally accepted and legally binding agreement on global climate change. It is a bridge between today’s and climate-neutrality policies and strategies before the end of the century. Critical to this endeavor is energy system modeling, which, while adept at devising cost-effective carbon-neutral strategies, often overlooks the broader environmental and social implications. This study introduces an innovative methodology that integrates life-cycle impact assessment indicators into energy system modeling, enabling a comprehensive assessment of both economic and environmental outcomes. Focusing on Switzerland’s energy system as a case study, the model reveals that optimizing key environomic indicators can lead to significant economic advantages, with system costs potentially decreasing by 15% to 47% by minimizing potential impacts from the current system still operating with fossil technologies to an alternative only relying on renewable and where the impact are mainly related to the construction of the infrastructure. However, a system optimized solely for economic efficiency, despite achieving 63% reduction in carbon footprint compared to 2020, shows a potential risk of burden shift to other environmental issues. The adoption of multi-objective optimization in this approach nuances the exploration of the complex interplay between environomic objectives and technological choices. The results illuminate pathways towards more holistically optimized energy systems, effectively addressing trade-offs across environmental problems and enhancing societal acceptance of the solutions to this century’s defining challenge.