The main chapel, the choir and the choir loft form the core of the Mosque-Cathedral. Leaving the choir, the chapels surrounding the nave can be seen; turning to the right, the first is the tombstone of the Five Bishops, executed in 1554 and made in marble according to the wishes of Bishop Leopold of Austria. It is followed by the chapel of the Dulce Nombre de Jesús, separated from the rest of the church by a magnificent grille. This is followed by the chapel of San Pelagio, the chapel of Santo Tomás and the chapel of Jesús, María and José, popularly known as the "chapel of the Lost Child". Past the transept, we reach the transept, covered by Gothic tracery decorated on the left side with busts of prophets, and on the right side with female figures, possibly representing the virtues.

The back part has five arches, four of which are chapels, the fifth being the entrance door to the sacristy. Above the arches there is a cornice with grotesques and tondos with busts, and on the five tympanums there are reliefs representing the 'Prendimiento', the 'Camino del Calvario', the 'Crucifixión', the 'Descendimiento' and the 'Resurrección', all anonymous works by a local workshop from the beginning of the 16th century, strongly influenced by the Flemish. Next to the sacristy door is the chapel of Saint Barnabas, followed by the chapel of the Guardian Angel, and then the chapel of the Presentation.

High altarpiece

The construction of the altarpiece of the Main Chapel began in 1618 and was designed in the Mannerist style by Alonso Matías.49 In 1627 the architectural work was continued by Juan de Aranda Salazar, and the altarpiece was completed in 1653.99 The sculpture was executed by the artists Sebastián Vidal and Pedro Freile de Guevara. The original paintings were by Cristóbal Vela and were replaced in 1715 by those of Antonio Palomino. The altarpiece is divided into three sections flanked by composite columns. The central body houses the tabernacle at its base, executed by Pedro Freile de Guevara, while the upper part contains a canvas of the Assumption. The side sections house canvases of the four martyrs: San Acisclo and Santa Victoria in the lower half and San Pelayo and Santa Flora in the upper half. The upper canvases are flanked by sculptures of Saint Peter and Saint Paul and the central part is crowned by a relief of God the Father.

Choir

The choir stalls, located in front of the main altarpiece, were made by Pedro Duque Cornejo between 1748 and 1757.4963100 The set was carved mainly in mahogany wood and presents a row of 30 chairs in the upper zone and another of 23 in the lower zone, all intricately decorated with reliefs, including a series of iconographic scenes. The reliefs on the upper section show the life of Jesus Christ on the right side and the life of the Virgin Mary on the left side, while the small medallions are all scenes from the Old Testament; the lower section also features scenes of the Cordovan martyrs. In the centre of the ensemble on the western side is a large episcopal throne, commissioned in 1752, which resembles the design of an altar. The lower part of the throne houses three chairs, although the most impressive element is the representation of the Ascension of Jesus that crowns it. The crowning figure is the sculpture of the archangel Raphael.