A method of manufacturing a Fabry-Perot interference filter includes a forming step of forming a first mirror layer having a plurality of first mirror portions, a sacrificial layer having a plurality of portions expected to be removed, and a second mirror layer having a plurality of second mirror portions on a first main surface of a wafer which includes parts corresponding to a plurality of two-dimensionally arranged substrates and is expected to be cut into the plurality of substrates along each of a plurality of lines; a removing step of simultaneously removing the plurality of two-dimensionally arranged portions expected to be removed from the sacrificial layer through etching after the Ruining step; and a cutting step of cutting the wafer into the plurality of substrates along each of the plurality of lines after the removing step.