A substrate processing apparatus is disclosed for bringing a substrate from a carrier, by a substrate transfer portion inside a transfer chamber, into a processing module to perform a process therein. The substrate processing apparatus includes a substrate storing chamber coupled to an exterior of the transfer chamber via a transfer opening to be in communications with the transfer chamber; a first storing shelf in the substrate storing chamber to store substrates for a first storing purpose; a second storing shelf in the substrate storing chamber to store substrates for a second storing purpose different from the first storing purpose; and a shifting mechanism that shifts the first and the second storing shelves to position a substrate storing area of one of the first and the second storing shelves so that substrate transferring is enabled between the substrate storing area and the substrate transfer portion via the transfer opening.