Buildings play a significant role in global carbon emissions, and offer substantial potential for energy savings and emission reduction. This research delves into the Emission Factor Discrepancy (EFD)—the variance in CO2 emission reduction projections obtained by employing either annual or hourly average Emission Factor (EF) for electricity generation. Through two detailed case studies in the Netherlands and incorporating emission data from the Netherlands, Sweden, and France, the study uncovers the potential magnitude and country-specific variability of the EFD. By demonstrating how the energy mix of a country influences the EFD, the research offers valuable insights into the accuracy of emission calculations for different circumstances, particularly in the context of transitioning to renewable energy sources. We have found that countries with energy sources having low load-following capability and low EFs exhibit a large EFD. Whereas, countries with high EFs and large deployment of Photovoltaics (PV) show a notably large EFD on emission reduction related to PV production. This highlights the importance of carefully selecting EFs when evaluating building retrofits in the context of smart city initiatives. This research highlights the need for establishing a uniform framework for calculating carbon emissions associated with retrofitting in buildings in conjunction with the granularity of data and the specific energy mix of a country.