As the EU energy system transitions to low carbon, the technology choices should consider a broader set of criteria. The use of Life Cycle Assessment (LCA) prevents burden shift across life cycle stages or impact categories, while the use of Energy System Models (ESM) allows evaluating alternative policies, capacity evolution and covering all the sectors. This study does an ex-post LCA analysis of results from JRC-EU-TIMES and estimates the environmental impact indicators across 18 categories in scenarios that achieve 80-95% CO2 emission reduction by 2050. Results indicate that indirect CO2 emissions can be as large as direct ones for an 80% CO2 reduction target and up to three times as large for 95% CO2 reduction. Impact across most categories decreases by 20-40% as the CO2 emission target becomes stricter. However, toxicity related impacts can become 35-100% higher. The integrated framework was also used to evaluate the Power-to-Methane (PtM) system to relate the electricity mix and various CO2 sources to the PtM environmental impact. To be more attractive than natural gas, the climate change impact of the electricity used for PtM should be 123-181 gCO(2eq)/kWh when the CO2 comes from air or biogenic sources and 4-62 gCO(2eq)/kWh if the CO2 is from fossil fuels. PtM can have an impact up to 10 times larger for impact categories other than climate change. A system without PtM results in similar to 4% higher climate change impact and 9% higher fossil depletion, while having 5-15% lower impact for most of the other categories. This is based on a scenario where 9 parameters favor PtM deployment and establishes the upper bound of the environmental impact PtM can have. Further studies should work towards integrating LCA feedback into ESM and standardizing the methodology.