A substrate processing apparatus includes a processing bath, a mixing device, a liquid path, and a silicon solution supply. A substrate is immersed in the processing bath to be processed. The mixing device generates a mixture liquid by mixing a phosphoric acid aqueous solution with an additive that suppresses precipitation of silicon oxide. The liquid path sends the mixture liquid from the mixing device to the processing bath. The silicon solution supply is connected to at least one of the liquid path and the processing bath, and supplies a silicon-containing compound aqueous solution to the mixture liquid supplied from the mixing device.