Hybrid electric aircraft with a powertrain based on fuel cells and batteries can reduce climate-active emissions in aviation. In a direct hybrid powertrain, the fuel cell and the battery are connected in parallel, without a DC/DC converter balancing their voltage levels. Switches make it possible to select different operational modes (fuel cell only, hybrid or battery charging) depending on the power demand during different flight phases. To exploit the high specific energy of hydrogen, the system should change from Hybrid Mode during take-off to Fuel Cell Mode in cruise. During descent, the battery can be charged if Charging Mode is selected. To avoid voltage and current peaks and consequent damage to components when switching between modes, certain conditions must be fulfilled. Those switching conditions were defined, and switching procedures for changing from one mode to the other during flight were developed and tested in a lab system. In a direct hybrid, the system voltage depends on the required power. When switching from Hybrid Mode to Fuel Cell Mode, a short reduction in power of 65% is necessary for the examined system to meet the switching requirements. It is also shown how this power loss can be reduced to 25% by distributed propulsion with a second powertrain or even eliminated by a change in the hybrid ratio.