There is provided a substrate processing apparatus having a transfer arm configured to transfer two substrates between a transfer chamber and a processing chamber having two mounting tables, the transfer arm holding the two substrates in a state where the two substrates overlap each other with a gap between the two substrates. The substrate processing apparatus includes: a lower substrate detection sensor configured to detect an edge portion of a lower substrate when the lower substrate is transferred; and an upper substrate detection sensor configured to detect an edge portion of an upper substrate when the upper substrate is transferred.