Provided are a method of manufacturing a semiconductor device capable of forming a high-quality film having low roughness and resistivity and a substrate processing apparatus and program. The method includes (a) forming an amorphous metal film on a substrate while maintaining the substrate by performing steps (a-1) and (a-2) in a time-divisional manner wherein the step (a-1) includes supplying in the time-divisional manner a metal-containing gas and a first reducing gas to the substrate a predetermined number of times to form a first amorphous metal film on the substrate, and the step (a-2) includes simultaneously supplying the metal-containing gas and a second reducing gas to the substrate having the first amorphous metal film formed thereon to form a second amorphous metal film on the first amorphous metal film; and (b) heating the substrate having the amorphous metal film formed thereon to.