To abate climate change and ameliorate the air quality in urban areas, innovative solutions are required to reduce CO2 and pollutant emissions from traffic. Alternative fuels made from biomass or CO2 and hydrogen can contribute to these goals by substituting fossil gasoline or diesel in combustion engines. Using a conjoint analysis approach, the current study investigates preferences of laypeople (n = 303) for fuel production facilities in terms of siting location, plant size, raw material used in the production, and raw material transport. The location was most decision-relevant, followed by raw material transport, whereas plant size and type of raw material played a less prominent role for the preference choice. The best-case scenario from the point of view of acceptance would be the installation of a rather small bio-hybrid fuel production plant in an industrial area (instead of an agricultural or pristine environment). No transport or transport via underground pipeline were preferred over truck/tank car or overground pipeline. The findings can be used as a basis for planning and decision-making for designing production networks for new fuel types.