A substrate processing apparatus includes a holder configured to hold a substrate; a driving unit configured to rotate the holder; an inner cup body provided in the holder to surround the substrate held by the holder; a mist guard, surrounding the holder and the inner cup body, configured to be moved up and down; a cleaning liquid supply configured to supply a cleaning liquid; and a controller. The controller is configured to perform: supplying a processing liquid to the substrate from a processing liquid supply, in a state that the substrate is held by the holder and the mist guard is raised; and dispersing, after the supplying of the processing liquid, the cleaning liquid supplied from the cleaning liquid supply to an entire inner peripheral surface of the mist guard, in a state that the substrate is carried out from the holder and the mist guard is raised.