A substrate processing apparatus configured to process a substrate includes a substrate holder configured to hold, in a combined substrate in which a first substrate and a second substrate are bonded to each other, the second substrate; a periphery removing unit configured to remove, starting from a periphery modification layer formed on the first substrate along a boundary between a peripheral portion to be removed and a central portion of the first substrate, the peripheral portion from the combined substrate held by the substrate holder; and a collection unit equipped with a collection mechanism configured to collect the peripheral portion removed by the periphery removing unit.