A substrate processing apparatus includes a first processing chamber and a second processing chamber, a first substrate holding unit that holds a substrate in the first processing chamber, a chemical solution supply unit that supplies a chemical solution containing an etching component and a thickening agent to the substrate held by the first substrate holding unit, a substrate transfer unit that transfers the substrate from the first processing chamber to the second processing chamber in a state in which the chemical solution is held on the substrate, and a second substrate holding unit that holds a plurality of substrates on each of which the chemical solution is held in the second processing chamber.