The restoration of the Cavaille-Coll Romantic organ housed in La Merced Church of Burgos, Spain is described in this paper. The organ was affected by a fire that took place in the church. The effect of the fire on the pipes differed depending on their location within the instrument. A combination of analytical techniques (X-ray diffraction, scanning electron microscopy with energy-dispersive X-ray analysis, particle-induced X-ray emission, metallography, and specific density) allowed the accurate determination of the microstructures and compositions of the alloys used to make the different pipes of the organ, some of which had a high tin content and others which had a high lead content. The most damaged pipes were replaced by reconstructed pipes made out of metallic sheets of the same composition as the originals, to ensure a historically accurate sound.