New propulsion technologies not only allow reducing the climate effect of aircraft, but also enable new architectures and integration options. To make use of this increased design space variety, new design methods need to be developed. In this work, an existing design process for CS-23 hydrogen-electric aircraft is expanded with the capability to design various powertrain options. These methods are used to evaluate the designs of two different concepts for small commuter aircraft with centralized and distributed fuel cell (FC) systems, respectively. The results show that the overall mass and performance of both concepts are very similar. However, the concept with distributed FC systems has a lower energy consumption, better FC cooling, and improved maintainability. Thus, the distributed concept is chosen. The final design has the powertrain components distributed among 10 engine pods. To transport nine passengers over 600 km without exceeding the targeted Maximum Take-off Mass (MTOM) of 5700 kg, the propulsion system’s power-to-weight ratio needs to be improved by 1.2% from the current technology level.