In front of the main altar, in the westernmost section of the Basilica, there is a Renaissance choir carved in Flanders oak wood, which includes choir stalls, a high cornice with mercy seat, the organ and a grille.

The choir stalls were made between 1542 and 1548 by Esteban de Obray, Juan de Moreto and Nicolás Lobato. It consists of three rows of seats superimposed in the form of tiers, arranged in an ultra-semicircular plan. In the lower part of the seats there is an inlaid work of yellow boxwood. Originally it had 138 seats, although today 124 remain, some of them reused on the sides of the presbytery of the main altar.

The iconographic program of the medioreliefs on the backrests is an outstanding work of the Spanish Renaissance. The main seats show scenes about the coming of the Virgin and the construction of the Holy Chapel by Santiago and the first converts, while the rest depict episodes from the life of Mary and the passion of Christ.

The main organ, whose case was described in 1610 as an "extreme sculpture" by Juan Bautista Labaña, was made in Plateresque style by Juan de Moreto and Esteban Ropic in 1529. It remained in its original state until 1940, when it was enlarged to cover classical and romantic repertoires, enlarging its case with decorations that imitate the original style.

The Mannerist railing, located in the choir, was created by Juan Tomás Celma between 1573 and 1578, with a marble base designed by Guillermo Salbán.