A method of operating a transport refrigeration unit that is operable to regulate a temperature of a cargo space. The method includes providing a controller, driving a refrigerant compressor of the transport refrigeration unit with an internal combustion engine to compress a refrigerant defining an engine operating state of the transport refrigeration unit, and driving the refrigerant compressor of the transport refrigeration unit with an electric motor to compress the refrigerant defining a motor operating state of the transport refrigeration unit. The method further includes sensing the temperature of the cargo space, receiving into the controller a signal indicative of the temperature of the cargo space, determining the temperature of the cargo space using the controller, and switching between the engine operating state and the motor operating state in response to a signal generated by the controller based on the temperature of the cargo space.