Systems and methods for operating aircraft power systems are disclosed. A power system in accordance with one embodiment of the invention includes an aircraft auxiliary power unit and a controller coupled to the aircraft auxiliary power unit, with the controller being configured to automatically stop the auxiliary power unit while the auxiliary power unit is functioning normally. The controller can also be configured to automatically start the auxiliary power unit in-flight when power supplied or expected to be supplied to a subsystem of the aircraft has a non-zero value at or below a threshold value. The controller may also be configured to start the auxiliary power unit when a load or expected load on the subsystem meets or exceeds a threshold value.