There are references to an organ as early as 1485 that indicate that previously there was one. In 1505, the City Council agreed to make a new one. A century later, in 1619, the Chapter commissioned another, having considered the organ to be of little power due to the large size of the church. This was built by Francisco Bordons and restored in the 18th century by Antonio Boscà. The organ suffered great damage in 1714 and 1808 and was finally destroyed during the Civil War.

In 1958, during the renovation of the presbytery of the basilica of Montserrat Abbey, the Puggina organ of 1922 was withdrawn and acquired by the Seu. In 1979, the organ suffered a fire that left it in poor condition. In 1988, the restoration and small extension of the instrument was inaugurated. In 2021, the Seu commissioned the organ workshop Carlos M. Álvarez, with the advice of the organist Marcel Martínez, a restoration and extension of the organ without losing its original essence. It was blessed and inaugurated during the centenary of the instrument.