A substrate processing apparatus includes a processing unit performing a predetermined processing on a substrate; a transfer chamber; and a substrate accommodation unit including a substrate accommodation chamber communicating with the transfer chamber via a transfer opening, a gate provided at the transfer opening to separate the substrate accommodation chamber from the transfer chamber, and a gas supply unit supplying a gas into the substrate accommodation chamber. The substrate accommodation chamber accommodates therein substrates that have been processed by the processing unit, and the gas supply unit provides a gas flow suppressing an atmosphere of the transfer chamber from being introduced into the substrate accommodation chamber, thereby preventing undesired reaction between moisture in the atmosphere of the transfer chamber and deposits adhered on the processed substrates accommodated in the substrate accommodation chamber.