A method of manufacturing an MEMS sensor according to the present invention includes the steps of: forming a first sacrificial layer on one surface of a substrate; forming a lower electrode on the first sacrificial layer; forming a second sacrificial layer made of a metallic material on the first sacrificial layer to cover the lower electrode; forming an upper electrode made of a metallic material on the second sacrificial layer; forming a protective film made of a nonmetallic material on the substrate to collectively cover the first sacrificial layer, the second sacrificial layer and the upper electrode; and removing at least the second sacrificial layer by forming a through-hole in the protective film and supplying an etchant to the inner side of the protective film through the through-hole.