In 1897 Aquilino Amezua signed a contract for 35,000 pesetas for the building of a new organ, taking full advantage of the beautiful original baroque case. In 1957 this instrument was moved to the central part of the choir from its previous location to one side of this. In 1986 it was restored by the Usabiaga brothers of Hernani, increasing the number of stops.
It has three manuals, each with a compass of 56 notes and one pedalboard of 30, with a total of 36 stops.