A method of manufacturing a Fabry-Perot interference filter comprising: a forming step of forming a first thinned region, in the forming step, a first mirror layer having a plurality of first mirror portions each of which is expected to function as a fixed mirror, a sacrificial layer having a plurality of portions expected to be removed, and a second mirror layer having a plurality of second mirror portions each of which is expected to function as a movable mirror are formed on a first main surface of a wafer expected to be cut into a plurality of substrates along each of a plurality of lines such that one first mirror portion, one portion expected to be removed, and one second mirror portion are disposed in this order from one substrate side, 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 the plurality of lines is formed; a cutting step of cutting the wafer into the 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 and extending a crack in a thickness direction of the wafer from the modified region, after the forming step; a removing step of removing the portion expected to be removed from the sacrificial layer through etching, between the forming step and the cutting step or after the cutting step; and characterized in that: wherein in the forming step: after a part along each of the plurality of lines in the sacrificial layer formed on the first mirror layer is thinned, side surfaces of the sacrificial layer and at least a portion of side surfaces of the first mirror layer facing each other along each of the plurality of lines are covered with the second mirror layer by forming the second mirror layer on the sacrificial layer. a forming step of forming a first thinned region, in the forming step, a first mirror layer having a plurality of first mirror portions each of which is expected to function as a fixed mirror, a sacrificial layer having a plurality of portions expected to be removed, and a second mirror layer having a plurality of second mirror portions each of which is expected to function as a movable mirror are formed on a first main surface of a wafer expected to be cut into a plurality of substrates along each of a plurality of lines such that one first mirror portion, one portion expected to be removed, and one second mirror portion are disposed in this order from one substrate side, 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 the plurality of lines is formed; a cutting step of cutting the wafer into the 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 and extending a crack in a thickness direction of the wafer from the modified region, after the forming step; a removing step of removing the portion expected to be removed from the sacrificial layer through etching, between the forming step and the cutting step or after the cutting step; and characterized in that: wherein in the forming step: after a part along each of the plurality of lines in the sacrificial layer formed on the first mirror layer is thinned, side surfaces of the sacrificial layer and at least a portion of side surfaces of the first mirror layer facing each other along each of the plurality of lines are covered with the second mirror layer by forming the second mirror layer on the sacrificial layer.