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. However, government and private companies still struggle to develop cost-effective carbon-neutral strategies. Energy system modeling has proved essential in creating strategies to generate carbon-neutral scenarios under minimal costs. However, cost minimization does not necessarily lead to publicly acceptable solutions nor generate configura- tions that minimize environmental impacts. Here we show a methodology to integrate LCIA indicators in an energy system model, assessing the impact of energy system configurations on economic and environmental aspects. Here we show a methodology to integrate life cycle assessment metrics in an energy system model to account for (i) emissions and impacts beyond the operation of the energy system itself and (ii) identify configurations optimizing both economic and environmental aspects. The model is applied to the case study of Switzerland and shows that with little modifications to the energy system configuration, carbon neutrality can be reached under the cost minimization objective while identifying trade-offs with other environmental issues. This work allows the generation of MOO of energy systems, minimizing burden shifting of environmental impacts and generating robust solutions for the energy transition, increasing social acceptance towards the biggest challenge of the 21st century.