Coupling life cycle assessment (LCA) and energy systems models (ESM) is a suitable approach to assess energy systems from both life cycle and energy systems perspectives. However, methodological challenges need to be taken into account due to differences between both modeling approaches considering system boundaries, databases, and different levels of detail of their input data. This paper brings these challenges into discussion and introduces the Environmental Assessment Framework for Energy System Analysis (EAFESA), which enables to identify life cycle based non-climate environmental impacts of energy scenarios consistently. EAFESA is applied to analyze potential future decarbonized European electricity systems with a focus on flexibility options using ELTRAMOD as an example of an ESM to test the conceptual approach of combining ESM and LCA. The application confirms the importance and benefits of "integrated thinking" proposed by EAFESA, which allows minimizing the pitfalls of combining both models comprehensively. At the same time, EAFESA has the potential to bring awareness of issues not discussed among policy-makers. One example is the insight that the decarbonized electricity system will be accompanied by increased metal demand and urban land occupation.