A substrate processing apparatus includes a substrate processing section that processes a plurality of substrates assuming a vertical posture in a batch manner; a first traversing mechanism that laterally moves a first traverse holding portion along a first traversing path between a substrate transfer position and a substrate delivery position; a second traversing mechanism that laterally moves a second traverse holding portion along a second traversing path disposed below the first traversing path between the substrate transfer position and the substrate delivery position; an elevation mechanism that raises and lowers an elevation holding portion in the substrate transfer position; and a main transfer mechanism that conveys a plurality of substrates assuming a vertical posture in a batch manner between the substrate delivery position and the substrate processing section, the first and second traverse holding portions, and the elevation holding portion each holds a plurality of substrates assuming a vertical posture in a batch manner.