A method of manufacturing a Fabry-Perot interference filter includes a forming step of forming a first thinned region, a first mirror layer, a sacrificial layer, and a second mirror layer are formed on a first main surface of a wafer, and the first thinned region in which at least one of the first mirror layer, the sacrificial layer, and the second mirror layer is partially thinned along each of a plurality of lines is formed; a cutting step of cutting the wafer into a plurality of substrates along each of the plurality of lines by forming a modified region within the wafer along each of the plurality of lines through irradiation of a laser light, after the forming step; and a removing step of removing a portion from the sacrificial layer through etching, between the forming step and the cutting step or after the cutting step.