A substrate processing apparatus includes: a processing chamber; a gas supplier configured to supply a gas into the processing chamber; and a controller. The controller is configured to control the gas supplier to perform: a) supplying a fluorine-containing gas into the processing chamber to clean an inside of the processing chamber; b) after a), supplying a reducing gas into the processing chamber to purge the inside of the processing chamber; c) after b), supplying a raw material gas and a reducing gas into the processing chamber to form a precoat film; and d) after c), supplying a reducing gas into the processing chamber to purge the inside of the processing chamber before depositing on a subsequent substrate. The controller is further configured to control the gas supplier to perform and stop c) based on the flow rates of the fluorine-containing gas and the raw material gas.