In the fund of the windchest the following inscription was found: “Lorenzo de Arrazo living near Oñate has been working on this organ in the year 1761.” The organ case was work of the masters Juan Antonio de Maíz and Joaquin Antonio Berasategui realised according to the plan arranged by the organ- builder. The organ is situated in a side of the chorus according to the tradition of the historic organs of Spain, Portugal and South America. In 1762, the organ expert Father José de Larrañaga approved the organ. Among its 1450 pipes, only 51 are just decorative. The organ has one manual (45 notes, C - c’’’) with “short octave” and eight diatonic pedal keys (C - H). A total of 35 stops is divided into 15 “Bajos” (left hand, C to c’) and 20 “Tiples” (right hand, c sharp’ to c’’’), plus a set of eight bass pipes. Above the console we find those typical spanish reed stops (trompetería de batalla). In addition the organ has some special effects: bird voice, drums and bass drums, as well as a reed stop (Corneta) enclosed in a swell box.

The organ has been restored in 1996 by the organbuilder José María Arrizabalaga, who in a careful work has reinstated its original characteristics. It is tuned in 1/5 comma meantone temperament.