A method performed by a film deposition apparatus including a process chamber and a rotary table that is disposed in the process chamber and includes a substrate-mounting surface on which a substrate is placeable. The method includes a first cleaning process of supplying a cleaning gas from above the substrate-mounting surface of the rotary table while rotating the rotary table in a first cleaning position, and a second cleaning process of supplying the cleaning gas from above the substrate-mounting surface of the rotary table while rotating the rotary table in a second cleaning position that is lower than the first cleaning position.