A substrate processing apparatus includes a substrate holder configured to horizontally hold and rotate a substrate which has a recess and a base metal layer exposed from a bottom surface of the recess; and a pre-cleaning liquid supply configured to supply a pre-cleaning liquid such as dicarboxylic acid or tricarboxylic acid onto the substrate being held and rotated by the substrate holder, to thereby pre-clean the base metal layer. A temperature of the pre-cleaning liquid on the substrate is equal to or higher than 40° C.