The organ of San Pedro y San Pablo Teposcolula is situated in a high left tribune originally connected by a narrow walkway to the choir loft. This allowed the Dominican friars direct access from the monastery to the loft and from there to the organ. It was eliminated for security reasons in 2010. The profile and overall shape of the organ are similar to that of Yanhuitlán, although on a more modest scale. Typical of many organs, it was not painted for years or centuries after the original construction (and many never were, for example Yucucuí). A Maltese cross painted on the first pallet indicates an 18th–century construction including baroque religious motifs such as the shell symbol of Santiago carved into the bases of the towers and the crest of the organ, topped with a cross, as well as a row of oval medallions across the façade. Documents refer to an indigenous organist from the community in 1597 and a repair in 1676, confirming the existence of a previous organ. 

In 1879, the instrument was drastically modified. Three of the ten original registers were canceled and others soon followed. The latest stop list used Puebla-style names. A pedal board was installed for a time, then later removed. The keyboard was rebuilt to resemble a piano keyboard. The damaged façade pipes were replaced with more resistant dark-colored zinc. The case and its unusually fine carved decoration were painted white (similar to Tlaxiaco) with light green and gold touches, probably during the 20th century, creating a tranquil look appropriate for the neoclassical era. In 2010 the fine carvings were gilded in order to make the organ look more impressive, but instead it made it look top-heavy. No physical or archival evidence existed to justify the organ's redecoration.