The organ of San Pedro Quilitongo is part of a group of four similar 8´ organs whose mechanics were built entirely or partially in a shop in Puebla and transported to Oaxaca. The case, built on site, has characteristic Oaxaca hips and a lambrequin decoration on the lower section. However, the upper case reveals Puebla influence: a curved upper profile, an upper case wider than the lower, rectangular (not Maltese) crosses painted on the roller board, and stop names particular to Puebla. Unlike the other similar organs, an unusually wide channel board rather than offset metal tubing fed the principal rank. 

The organ is disproportionately large for its church and was apparently acquired from another church also dedicated to Saint Peter sometime during the 20th century. An informant mentioned that the roof of the choir loft had been raised to accommodate the tall organ. Symbols of Saint Peter, the papal miter and the keys to heaven, similar to the organ in San Pedro Ozumacin, as well as a rectangular cross in the crest, are carved above the central tower. In contrast, religious symbols were rare in Oaxaca-built organs at this time. In 2008 the IOHIO recovered and attached most of the carvings to the upper case.