Reducing aviation emissions is important as they contribute to air pollution and climate change. Several alternative aviation fuels that may reduce life cycle emissions have been proposed. Comparative life cycle assessments (LCAs) of fuels are useful for inspecting individual fuels, but systemwide analysis remains difficult. Thus, systematic properties like fleet composition, performance, or emissions and changes to them under alternative fuels can only be partially addressed in LCAs. By integrating the geospatial fuel and emission model, AviTeam, with LCA, we can assess the mitigation potential of a fleetwide use of alternative aviation fuels on 210 000 shorter haul flights. In an optimistic case, liquid hydrogen (LH2) and power-to-liquid fuels, when produced with renewable electricity, may reduce emissions by about 950 GgCO2eq when assessed with the GWP100 metric and including non-CO2 impacts for all flights considered. Mitigation potentials range from 44% on shorter flights to 56% on longer flights. Alternative aviation fuels’ mitigation potential is limited because of short-lived climate forcings and additional fuel demand to accommodate LH2 fuel. Our results highlight the importance of integrating system models into LCAs and are of value to researchers and decision-makers engaged in climate change mitigation in the aviation and transport sectors.