The organ of Santiago Tejupan is extravagant both in decoration and construction, thanks to the financing by a wealthy man in the community. Medallions carved on the façade cite the donor's name, Nicolas Ruis [sic], that of his wife Barbara, the date of the organ's construction, and its cost. Unfortunately, but typically, the organ builder is not identified. In addition, portraits of Nicolas and Barbara are painted on the left side of the organ case, together with his patron saint, San Nicolas de Tolentino. Saint James (Santiago), the patron saint of the community, is depicted on horseback on the right side, barely visible under layers of grime. This organ is the last in Oaxaca painted with religious figures. Maltese crosses would surely have existed on a pipe or pallet, but the pieces no longer exist. Like the Huayapam organ, it was varnished in the 20th century, which darkened the original bright colors of the painted decoration; neglect has darkened it even further. 

The organ had two complete reed ranks jutting out from the façade: the customary row of clarines and another row below it of wooden reed pipes labeled "tolosano," unique in Oaxaca. Another unexpected feature was its direct suspended action with no roller board, as indicated by one remaining very long tracker. A solitary non-speaking façade pipe decorated with a face and flowers is a reminder of the organ’s original opulence. The bellows were nearly burned up with discarded church items in 2000, but were rescued from the wood pile as a curiosity, not because they recalled an organ.