A substrate processing apparatus includes a processing unit and a control unit. The processing unit is configured to perform an etching processing by immersing a substrate in a processing liquid containing phosphoric acid and a silicon-containing compound. The control unit is configured to control the processing liquid such that the substrate is processed, in a first processing time of the etching processing, with the processing liquid having a first phosphoric acid concentration and a first silicon concentration, and the substrate is processed, in a second processing time later than the first processing time, with the processing liquid having a second preset phosphoric acid concentration lower than the first phosphoric acid concentration and a second preset silicon concentration lower than the first silicon concentration or with the processing liquid having the second preset phosphoric acid concentration and the first silicon concentration.