A substrate processing apparatus includes a first atmosphere control system configured to control an atmosphere inside a processing zone of a substrate processing area and a second atmosphere control system configured to control an atmosphere inside a substrate transfer zone of the substrate processing area. The first atmosphere control system supplies, when a liquid processing is performed in a liquid processing unit, an atmosphere control gas to the corresponding liquid processing unit by a first gas supply, and discharges an atmosphere inside the corresponding liquid processing unit by a first gas discharge unit. The second atmosphere control system circulates an atmosphere adjustment gas in a circulation system of the corresponding second atmosphere control system, and discharges an atmosphere inside the circulation system of the second atmosphere control system when at least one of the liquid processing unit is opened to the substrate transfer zone.