Reconstruction: 1996-1997 by Susan Tattershall (Órganos Históricos de México). The case was restored by SEDUE (Secretaría de Desarrollo Urbano y Ecología) in 1990 and by Miguel Villeda in 1996; the new pipes were built by Pascal Boissonet. The project was funded by the J. P. Morgan Foundation.

Located in a high tribune on the right side of the nave, the small organ of Santa María Natividad Tamazulapan is one of a group of six 2´ table organs from the Mixteca Alta region of Oaxaca that are nearly identical in construction. It is the smallest of the six with the finest case painting, and it is the only organ restored and playable. It is decorated all over with religious imagery: left side, Saint Francis; left door exterior, Saint Nicholas of Bari; left door interior, angel musician playing a lute; right door interior, angel musician playing a viola da gamba; right door, Saint Antoninus of Florence; right side, Saint Anthony of Padua. The case, table, and top and bottom pieces of the bellows are original. The pipes, keyboard, windchest, and mechanics were rebuilt. This is the only playable Oaxaca organ without a blower for the bellows, so it must be hand pumped. The organ faces a large, unrestored 19th century organ across the nave.