A substrate processing apparatus includes a plurality of arms used for transferring a substrate, a plurality of processing sections for processing the substrate, a recipe storage section storing at least one recipe for designating at least one of the plurality of arms as a usable arm and at least one of the plurality of processing sections as a usable processing section and for specifying processing conditions in the usable processing section, and a control unit for, according to the at least one recipe, controlling the plurality of arms and the plurality of processing sections so that a substrate is transferred using the usable arm and is processed in the usable processing section under the processing conditions.