The case of the organ of Santiago Lachiguiri is made of cedar and well preserved. It is rather large for a 4´ organ, the lower case is narrower than the upper, and the three façade towers are flat. The fine neo-classical decorative carvings above the towers and the carved lambrequin design under the keyboard are characteristic of early 19th-century Oaxaca organs. Offset metal tubing for the principal stop indicates the influence of Puebla organbuilding. 

During our first visit in 2001, the IOHIO discovered four table clavichords encased in wooden boxes resting against the wall of the choir loft. They were varying degrees of repair and only one still had its keyboard and strings. Two of the other three clavichords documented in Mexico are in museums, and the third, just an empty frame, is in the Oaxaca community of Santa María Pápalo. Four decorated organ pipes with faces similar to those of Tlacochahuaya and Quiatoni most likely belonged to the previous 18th century organ baroque organ. A collection of band instruments, from the late 19th or early 20th century, was piled up in the choir loft. The combination of an extant organ, evidence of a former organ, the clavichords, and the band instruments attest to a rich musical life in times past in this rather remote community. 

During the 2017 earthquake, the church, including the roof over the choir loft, was severely damaged. The organ was dismantled by the INAH in 2019, packed up, and stored in the sacristy; its fate is impossible to predict. 

Four decorated pipes seem to belong to an earlier organ.