Provided are a method of manufacturing semiconductor device, a substrate processing apparatus and a recording medium which are capable of efficiently removing a deposited film in a shower head and suppressing generation of particles. The method of manufacturing a semiconductor device includes (a) forming a film on a substrate by supplying a film forming gas and an inert gas to the substrate in a processing chamber via a shower head, and (b) removing a deposited film deposited in the shower head in (a) by supplying to the shower head an inert gas, which has a temperature lower than that of the inert gas supplied in (a), into the shower head without the substrate loaded in the processing chamber.