A flash lamp system provides flashes to a bottom side of a conveyor to disinfect the conveyor while the conveyor is transporting products on a top side of the conveyor. The flashes are provided to discontinuous segments of the conveyor such that a portion of the conveyor is treated with each revolution, but a controller causes the entire length of the conveyor to be disinfected over multiple revolutions. The controller can respond to changes in speed and detected levels of disinfection. The disinfection system can be used in many applications, such as the transporting of fresh or frozen food products.