The escalating urgency of climate change, alongside the directives of the European Union’s (EU) Energy Performance of Buildings Directive (EPBD), necessitates the advancement of the Zero Emission Building (ZEB) assessment framework. A pivotal aspect of ZEB qualification is the enhancement of its analysis methodology. This study presents a new proposal methodological approach for the evaluation of ZEBs through Life Cycle Analysis (LCA) in compliance with the EN 15978 standard. Our proposed methodology facilitates an accurate assessment of the Global Warming Potential (GWP) indicator for existing nZEBs. The methodological steps include: first, calculating the GWP during the operational phase of the building via a calibrated dynamic simulation using Design Builder, which generates precise energy consumption data. This data, coupled with the emission conversion factor specified by Spanish regulations, enables the determination of the equivalent kgCO2 emissions for the building’s use phase. Additionally, we evaluate the GWP embedded in the construction and material transport phases by compiling a detailed inventory of the building’s construction materials and incorporating their Environmental Product Declarations (EPDs). The total GWP is computed by aggregating the operational and embedded GWP indicators, providing a holistic evaluation of the ZEB’s environmental impact. Our case study demonstrates that the construction phases and material transportation significantly influence the building’s overall environmental performance. This research highlights the critical need to address both operational and embedded emissions to achieve authentic Zero-Emission Buildings.