The organ of San Mateo Yucucuí is the least altered and most complete of Oaxaca's surviving 8´ stationary instruments. Nearly 80% of its pipes survive; most are piled up inside the case after their thin supporting rackboards fell apart. Unfortunately, because of the precarious position of the organ in a high, narrow tribune and the deterioration of the support beams underneath, it has not been possible to properly conserve the organ or attach the loose carvings stored inside the case. On the other hand, because of its inaccessibility, the interior of the organ is in excellent condition. The keyboard is complete, restored or rebuilt in 18th-century style sometime during the 19th century. The date of construction, 1743, is inscribed on the central facade pipe; Maltese crosses are painted on the first trundle and the first pallet of the windchest. The façade highlights two of the baroque medallions, one round and one oval, and the fine open-work carving. The carved adornment on the crest is missing and may or may not exist. The two small side towers are decorative with dummy pipes. This organ was probably intended to be painted and gilded at some point, to complement the baroque altarpieces in the church. But the project was never realized, undoubtedly because of a lack of funds. 

Because of its location on a promontory overlooking part of the Nochixtlan Valley, the sound of the organ was apparently heard for miles around. Inscriptions inside the case indicate that it was repaired and played regularly. In 1876, an inscription on the roller board indicates that Don Pantaleón Cano, a member of the Cano family of organbuilders, tuned the organ; he also may have made the new labels. In 1926, a detailed document inside the case indicates that the organ builder Juan E. Silva from Guerrero tuned and repaired the pipes. He also intervened in the Tiltpec organ, presumably around the same time.