In a method of manufacturing an electronic component built-in substrate of the present invention, a mounted body including a first insulating layer, a stopper metal layer formed under the first insulating layer of a portion corresponding to a component mounting region and a second insulating layer formed on a lower surface of the first insulating layer and covering the stopper metal layer is prepared, and a concave portion is obtained by penetration-processing a portion of the first insulating layer, which corresponds to the component mounting region to form an opening portion, while using the stopper metal layer as a stopper. Also, the stopper metal layer in the concave portion is removed, then an electronic component is mounted on the concave portion, and then a third insulating layer is formed on the electronic component.