The organ of San Miguel Arcángel Tlalixtac was one of Oaxaca’s grandest 19th-century instruments, and its sound was apparently heard for miles around. Its design is unusual, with the imposing upper case resting on the hips of the lower. A wider lower case in proportion to the upper would have adhered to the traditional style of Oaxaca organ building. But this organ serves as yet another example of departing from the norm, usually justified by lowering the cost of the project. It is rather hard to imagine the visual impact of this organ in its current deteriorated state, especially with the metal pipes of the central tower missing and only the previously hidden wooden bardón pipes visible. The keyboard of the Tlalixtac organ may be the first built in Oaxaca to reach 56 notes, which eventually became standard. A punched (repussé) rectangular cross on a metal bardón pipe indicates a Puebla intervention, perhaps by the pipe builder; otherwise there are no signs of Puebla influence. The lower case façade is beautifully embellished with sinuous carvings synchronized with the curved side profile. The interior pipes were arranged in five pyramids, and the 8´ horizontal trumpets were spread across the façade in five pointed groups. The roller board is still in good condition compared to the rest of the organ since it faces inward. 

Once the organ began to deteriorate and the community was no longer obligated to pay for its maintenance after Vatican II in the 1960s, the dismembering process began. Many large façade and trompeta real pipes survive, but because of their high lead content, they are malleable and too fragile to straighten. Even if they did, the support structures no longer exist in the empty towers. In 1674, the Dominican friar Francisco de Burgoa referred to an organ and praised the excellent musical activity in Tlalixtac. This confirms that the current organ had at least one baroque predecessor.