Provided are a substrate processing apparatus, a method of manufacturing a semiconductor device, and a non-transitory computer-readable recording medium, which are capable of reducing an effect on a substrate, which is caused by a change in an atmosphere in a substrate storage container, by appropriately supplying an inert gas into the substrate storage container. The substrate processing apparatus includes a purge mechanism installed in at least one of a support unit and a receiving unit accommodating a substrate storage container, and configured to supply an inert gas into the substrate storage container; a monitoring unit configured to compare a flow rate of the predetermined gas supplied into the substrate storage container via the purge mechanism with a preset reference value and output a signal indicating a result of comparison between the flow rate of the predetermined gas and the preset reference value; and a management unit configured to manage use of the substrate storage container, based on the signal outputted from the monitoring unit.