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With an increasing share of renewable energy technologies in our energy systems, the integration of not only direct emission (from the use phase), but also the total life cycle emissions (including emissions during resource extraction, production, etc.) becomes more important in order to draw meaningful conclusions from Energy Systems Analysis (ESA). While the benefit of integrating Life Cycle Assessment (LCA) into ESA is acknowledged, methodologically sound integration lacks resonance in practice, partly because the dimension of the implications is not yet fully understood. This study proposes an easy-to-implement procedure for the integration of LCA results in ESA based on existing theoretical approaches. The need for a methodologically sound integration, including the avoidance of double counting of emissions, is demonstrated on the use case of Passivated Emitter and Rear Cell photovoltaic technology. The difference in Global Warming Potential of 19% between direct and LCA based emissions shows the significance for the integration of the total emissions into energy systems analysis and the potential double counting of 75% of the life cycle emissions for the use case supports the need for avoidance of double counting.