The subject matter of this specification can be embodied in, among other things, a method for operating a hydraulic free piston engine includes receiving, at an engine controller for a hydraulic free piston engine, an energy parameter that is representative of an amount of fluid energy to be output by the engine, and a measured fluid pressure value of a fluid load of the engine, determining a piston trajectory of a piston within a hydraulic chamber of the engine, determining a fuel volume value and a servo valve actuation parameter, based on the energy parameter and the measured fluid pressure value, providing a fuel control signal to a fuel control device of the engine based on the fuel volume value, and providing, based on the servo valve actuation parameter and the piston trajectory, a servo valve control signal to a servo valve.