Emissions from aviation contribute increasingly to air pollution and climate change. Several alternative aviation fuels that may reduce life-cycle emissions have been proposed, but most comparative assessments of these disregard a variation of the mitigation potential with flight distance, highly relevant short-lived climate forcings, and changes to aircraft design. To address these gaps, we integrate a geospatial fuel and emissions model into a life cycle assessment and assess the mitigation potential of alternative aviation fuels on 210,000 shorter-haul flights. We find that in an optimistic case, liquid hydrogen and power-to-liquid fuels' mitigation potentials range from 44% on shorter flights to 56% on longer flights in the GWP100 metric. The mitigation potential is limited because we include short-lived climate forcings with up-to-date impacts and assume a shorter mean flight distance. These findings are important to researchers and decision-makers engaged in climate change mitigation in the aviation and transport sector.