A substrate processing apparatus includes a substrate processing part that supplies a processing liquid from a processing liquid supply part to a mounted substrate to execute liquid processing, a liquid drainage part that has a recovery channel connected to a storage part that stores the processing liquid and drains the processing liquid used for the liquid processing, and a control unit executes a processing recipe for the liquid processing and a cleaning recipe for cleaning the substrate processing part and the liquid drainage part. The control unit executes a cleaning operation for supplying a cleaning liquid from a cleaning liquid supply part to clean the substrate processing part and the liquid drainage part and subsequently executes a return operation for supplying the processing liquid from the processing liquid supply part to replace the cleaning liquid attached to the substrate processing part and the liquid drainage part with the processing liquid.