Organs have always been among the most important musical instruments in Europe. Because of their highly complex mechanical systems and the wide variety of materials they are made of, such as metal, ivory, wood or paperboard, they are considered one of the hardest instruments to preserve. Particularly, the different materials used to make the pipes, mainly tin or lead alloys, are sensitive to environmental conditions such as temperature and moisture, and consequent decay. The alteration processes are mostly due to tin-pest development or to the oxidation. As a consequence, sound quality decreases or, in the worst cases, pipes are completely lost. The aim of this work is to investigate several Italian pipe fragments dating from the seventeenth to twentieth century, in order to: (1) analyse the raw materials and the traditional manufacturing of organ pipes, in relation to conservation issues; (2) characterize the particular decay processes; (3) outline a suitable methodological approach to characterize the most common alterations of metal organ pipes. For this purpose, during the analytical campaign, both non-invasive and micro-destructive methodologies were performed, i.e. stereomicroscopy observations, X-ray fluorescence analysis, scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy analysis and X-ray diffraction. The application of the proposed analytical procedure allowed the differentiation of the pipe fragments examined into several groups on the basis of original materials and morphological characteristics.