Today's energy systems are dominated by finite fossil fuels and related environmental and human health impacts. To strive for the Sustainable Development Goal (SDG) related to energy, their transformation must be initiated. Insights on the sustainability of energy system transformation pathways can be gained by combining partial equilibrium energy system modelling and life cycle assessment (LCA) due to their complementary characteristics. The present study aims at demonstrating an approach on how LCA indicators can be quantified for the integration in partial equilibrium energy system models without double-counting of impacts of the energy system and how such analyses can be used to estimate environmental and human health impacts of energy system transformation pathways. The results for the World Energy Scenarios show that the environmental and human health "hotspots" are coal (mining, heat and power generation, ash disposal), oil (freight and passenger transport, industrial motors) and biomass (cultivation, heat generation, ash disposal) technologies. The regional results are found to be more informative than the global results, also because many environmental and human health indicators reflect regional impacts. The transformation pathway with a focus on climate change mitigation policies has co-benefits regarding environmental and human health impacts and thus contributes to several SDGs, while it encounters challenges related to water and land use.