Restoration: 1990-1991 by organ builder Susan Tattershall; the case and façade pipes were restored by Mireya Olvera; reconstruction of the missing pipes by organ builder Joachium Wesslowski. The project was funded by the Pichiquequiti Foundation.

The organ of San Jerónimo Tlacochahuaya is one of the most beautiful and also one of the most enigmatic of Oaxaca’s baroque instruments. Unfortunately, the construction date and the builder’s name are unknown, and the documents from the 18th century and before are missing from the parochial archive.  The organ shares characteristics of musical design and case decoration with those in San Dionisio Ocotepec, San Andrés Zautla, and San Pedro Quiatoni (1729). Each of these confirms the construction date on a pipe or on a label in the chest, which helps assign an approximate construction date for the Tlacochahuaya organ. The faces and floral decoration painted on the façade pipes are very similar to those of the Quiatoni table organ, suggesting that the organs might have been built around the same time, even in the same shop. Soon after their construction, the Tlacochahuaya and Quiatoni organs were modified.  Only one early date appears on the Tlacochahuaya organ, 1735. It was inscribed on the first pipe of the bass octave of an 8´ stopped flute register (bardón), which was added to the existing 4´ flute (tapadillo) to lower the tonal base and enhance the sound of the organ. A Maltese cross appears above the date and also on the ninth bardón pipe, which had been the first of the former tapadillo rank. To further reinforce the organ’s sound, the drum stop on the left was canceled, and a 4´ reed stop (bajoncillo) was installed (21 notes C-c’) in its place. These modifications were replicated in the Quiatoni organ with 13 rather than 21 notes probably around the same time.

The bajoncillo is usually positioned horizontally on the façade of the organ; a vertical placement inside the case is unusual. The Quiatoni table organ lacked a façade to permit any further upgrades, although it is the only table organ in Oaxaca with a bajoncillo interior reed. Photos of the interiors of both cases reveal that they were equally crowded with new pipes. Like the stationary organ in Ocotepec, Tlacochahuaya’s had direct suspended key action with a Maltese cross on the first pallet. The stop action was controlled by slider tabs protruding from the sides of the case. Such action was not typical of stationary organs and may mean that the organ was originally a table organ.  However, there is no evidence of front doors in the Tlacochahuaya organ, although the Ocotepec organ, originally from the neighboring town of Tlacolula, did have doors. Perhaps both organs (and Quiatoni, as mentioned above) were produced in a shop in Tlacolula, the predominant community in the region. 

The date 1737 is inscribed above the entrance to the church, celebrating the extension and brick roofing of the nave, the new façade, the new choir loft, and the interior decoration. Before this date, the organ would have been situated on the church floor and later moved up to the choir loft. A large window illuminates the area and would have had protective doors. Even then, rain water could flood the floor from under the doors and through the window at the top of the stairway, so the organ and the bellows were situated on a cement base for protection. Additional undated 18th-century modifications include the installation of the treble half of the clarín on the façade of the organ, even though it did compromise the overall design. The rack supporting the clarin trumpets was nailed onto the top row of medallions, obscuring half of it in shadow. The stop action was moved to the façade, as indicated by the current stopknobs, and the mechanics were rebuilt with rotating trundles in the interior. The previous system with slider tabs was canceled, except for the right–hand bird (pajaritos) stop. All these changes require a stronger base to sustain the weight of the added pipes and the heavier more complicated stop action. So if it was originally a table organ, by the mid-18th century it would have been converted to a stationary organ with a new lower case.  These adjustments were surely complicated and expensive. The funding may have come from a wealthy donor or his estate, as in the Soledad organ, or from donations collected by the church brotherhoods (cofradías) from the community, wealthy at the time because of the cochineal trade. Yet by 1806, when Oaxaca’s robust economy began to decline, farmers in the community contributed $40 pesos to repair the organ from the sale of three cartloads of corn from church lands 

The organ was played and maintained regularly throughout the 19th and 20th centuries, as noted in the church account book for repairs and payments to the organist. The most specific reference appears above the Maltese cross on the first bardón pipe, a repair by the organ builder José Ignacio Sánchez in 1867. He was well-known and intervened in many Oaxaca organs during the later 19th century. The fact that he inscribed his name on the pipe implies that this intervention was more complex than just a tuning. He may have made the new keyboard, rebuilt the bellows with leather, and more. The organ case we see today is profusely decorated with billowing floral motifs, which harmonize with the colorful interior of the church. The pipeshades include fine open-work carvings that also adorn the periphery of the case. Angel musicians grace the sides, on the right playing a violin and on the left a lute. The organ is crowned with an image of Saint Jerome in a medallion above the central tower.