The paper presents a power electronic conversion system and its control for a fuel cell and a battery-based hybrid drive system for a motor glider. The energy conversion system is designed in such a way that the fuel cell gives power equal to the electric drive power demand for horizontal flight, whereas during motor glider take-off and climbing, the fuel cell is supported by the battery. The paper presents the power demand related to the assumed mission profile, the main components of the hybrid drive system and its holistic structure, and details of power electronics control. Selected stationary experimental test results related to the energy conversion and drive system are shown. Some results related to the aircraft tests on a runway are presented.