A method of manufacturing a photoelectric conversion apparatus which includes a pixel circuit section having a well where a photoelectric conversion element and an amplification element configured to generate a signal based on an amount of charge generated in the photoelectric conversion element are arranged, and a peripheral circuit section having a MOS transistor. The method includes forming a dielectric film for covering the photoelectric conversion element, the amplification element, and a gate electrode of the MOS transistor and forming, by etching the dielectric film, a side spacer by remaining a portion of the dielectric film on a side surface of the gate electrode while protecting by a resist, wherein an opening is formed in the dielectric film of the pixel circuit section with the etching, and a contact for defining a potential of the well is formed through the opening.