A substrate processing apparatus includes: a chamber having at least one gas inlet and at least one gas outlet; a substrate support disposed in the chamber; and a controller. The controller causes (a) placing a substrate on the substrate support, the substrate including a base layer and a first layer formed on the base layer; (b) etching the first layer to form a recess in the first layer; (c) when determined that the recess satisfies a predetermined condition, forming a first film on a bottom surface of the recess by forming an inhibitor on the bottom surface of the recess, a predetermined gas species being not adsorbed to the first film; (c) after (b), forming a second film on a side wall of the recess using the predetermined gas species as a precursor gas; and (d) etching the first layer through the recess.