An electronic device may have electrical components mounted in alignment with an electronic device housing. A compass in the electronic device housing may potentially be misaligned with respect to the electrical components and the electronic device housing. Reference devices having compasses may be used to gather compass data while one or more electrical components in the reference devices are controlled to generate magnetic fields that are detected by the compasses. An electronic device may be calibrated in a factory or in the field using calibration data produced by comparing compass readings gathered from the compass in the device while controlling electrical components in the device to compass data from the reference devices. Calibration data may be applied to compass readings in real time to correct for misalignment between the compass and the electronic device housing.