Disclosed is a substrate processing apparatus including: a holding unit configured to hold a substrate; a processing liquid supply unit configured to supply a first processing liquid and a second processing liquid to the substrate; a first cup configured to recover the first processing liquid; a second cup disposed adjacent to the first cup and configured to recover the second processing liquid; a recovery portion defined by a peripheral wall portion that is erected on a bottom portion of the first cup; and a cleaning liquid supply unit configured to supply a cleaning liquid to the recovery portion. The peripheral wall portion is cleaned by causing the cleaning liquid supplied by the cleaning liquid supply unit to overflow from the peripheral wall portion to the second cup side.