A substrate processing apparatus includes a substrate rotator that holds and rotates a substrate including a film of a metal formed on a surface thereof, a first supply that supplies a first processing liquid containing a chelating agent and a solvent toward the substrate, a second supply that supplies a second processing liquid containing water toward the substrate, and a controller that controls the substrate rotator, the first supply, and the second supply. While rotating the substrate by the substrate rotator, the controller supplies the first processing liquid toward the substrate by the first supply to generate a complex containing the metal and the chelating agent, and after the generation of the complex, supplies the second processing liquid toward the substrate by the second supply to dissolve the complex in the second processing liquid.