An imaging system may include a camera module with an image sensor having an array of image sensor pixels and one or more lenses that focus light onto the array. The system may include processing circuitry configured to mitigate flare artifacts in image data captured using the array based on at least one image flare map. The image flare map may identify a portion of the captured image data on which to perform image flare mitigation operations. The processing circuitry may perform image flare mitigation operations such as pixel value desaturation on the identified portion of the captured image data without desaturating portions of the image data that do not include flare artifacts. The flare map may be generated using a calibration system that characterizes the location, intensity, and color of all possible image flare artifacts that may be generated by the imaging system during normal imaging operations.