Due to the continuous diurnal, seasonal, and annual changes in the German power supply, prospective dynamic emission factors are needed to determine greenhouse gas (GHG) emissions from hybrid and flexible electrification measures. For the calculation of average emission factors (AEF) and marginal emission factors (MEF), detailed electricity market data are required to represent electricity trading, energy storage, and the partial load behavior of the power plant park on a unit-by-unit, hourly basis. Using two normative scenarios up to 2050, different emission factors of electricity supply with regard to the degree of decarbonization of power production were developed in a linear optimization model through different GHG emission caps (Business-As-Usual, BAU: −74%; Climate-Action-Plan, CAP: −95%). The mean hourly German AEF drops to 182 gCO2eq/kWhel (2018: 468 gCO2eq/kWhel) in the BAU scenario by the year 2050 and even to 29 gCO2eq/kWhel in the CAP scenario with 3700 almost emission-free hours from power supply per year. The overall higher MEF decreases to 475 and 368 gCO2eq/kWhel, with a stricter emissions cap initially leading to a higher MEF through more gas-fired power plants providing base load. If the emission intensity of the imported electricity differs substantially and a storage factor is implemented, the AEF is significantly affected. Hence, it is not sufficient to use the share of RES in net electricity generation as an indicator of emission intensity. With these emission factors it is possible to calculate lifetime GHG emissions and determine operating times of sector coupling technologies to mitigate GHG emissions in a future flexible energy system. This is because it is decisive when lower-emission electricity can be used to replace fossil energy sources.