Alfonso VII of León and Castile (1126–1157) granted privileges and donations to increase the population, unifying two towns: the upper around the castle and the lower one, the Mozarabic, around the channel of the Henares River.

[5] A document from 1144 says that Bernard of Agen rebuilt a primitive cathedral "with a double wall and tower," possibly on the remains of an old Visigothic or Mozarabic church, Santa María Antiquíssima.

[10] The middle door, called the "Puerta de los Perdones,"[11] is built with a semicircular arc and archivolts supported on columns with a capital.

Above it is a pediment with a medallion in Baroque bas-relief representing the scene of The imposition of the chasuble on Saint Ildefonsus and a Romanesque rose window of the 13th century to illuminate the central nave.

In the central nave (higher), you can see the Gothic ogival stained glass, separated by buttresses, with the eaves, resting on brackets, with animal forms, alternating with metopes decorated with plant motifs.

The cathedral, is currently composed of a Latin cross plant, with three naves, ample transept and head with a large apse, which it contains the main chapel, surrounded by the ambulatory.

Three of the four pillars that frame the choir are different from the rest of the building, consisting of large cylindrical columns with Romanesque ornamentation in the lower part and Gothic in the upper one.

The main altar presides over an image of Saint Peter, and under this statue is the Santísima Trinidad work of the sculptor Mariano Bellver y Collazos of 1861, carved in wood and polychrome.

It is located on an arch that gives way to the baptistery and in front of the viewer, it was probably moved from its original place during the works of the 17th century, you can read an inscription that says: "El señor obispo Lujan.

[19] It shows a mixture of styles such as Renaissance pilasters, Mudéjar arabesques and Gothic arches, although it is from the beginning of the 16th century, it was built by Domingo Hergueta.

This door gives entrance to the cloister, where is the chapel of San Valero, the oldest in the cathedral, with a Romanesque floor and a Gothic iron gate.

[16] Founded in 1515 by the provisor Fernando Montemayor, its magnificent portal is decorated to the "Cisneros style",[20] consists of a low part of Plateresque pilasters where small niches are found that house images of Saint Michael and Saint James, in the arch the ornamentation is composed of geometrical Mudéjar elements of intersecting lines, forming figures of starred laqueus and polygonal between which are shields of the founder of the chapel and in the frieze that also follows it of laqueus is the shield of the cathedral chapter with a scene of The Annunciation under Gothic arches, topped by a cornice, very decorated of Arab type, with a figure of lion, in each end, the crowning of the portal constitutes some arcs in Gothic style with the representation of a Calvary in the central point.

[23] This nave of the Gospel ends with the altars, of Saint John the Baptist formed with a Plateresque arch made by Francisco de Baeza in 1530 and with a Baroque altarpiece of the 18th century.

In the lower part, behind the reredos and inside the semicircular arch, is where the altarpiece itself is, formed by two bodies and three streets, the central one wider and higher than the lateral ones, with six paintings on a table of Juan Soreda made between 1525 and 1528.

It was the moralizing message of Renaissance to present the exemplary life of Wilgefortis and her sisters, [28] as Santiago Sebastián says: ... for to express that she was as virtuous and strong as Hercules himself.

The entrance to the chapel is made through an iron gate executed by Juan Francés between 1526 and 1532, the portal is Plateresque style and was built by Francisco de Baeza.

[31] The sepulcher placed on three lions is under a niche in semicircular arch, with the statue of the doncel in alabaster, is dressed in armor and with the cross of Saint James in the chest, the fist of a sword and a small dagger can be seen in the waist, the head is covered with a bonnet that fits completely, but what stands out most is that it is not a recumbent figure, asleep, but that he is reclining, with one leg over the other and supports the half-built arm, in the attitude of reading a book that he holds open in his hands, in the front of the tomb two pages hold the coat of arms and it is ornamented with delicate carvings in candilieri.

The lower part of the niche, contains the following inscription:Here lies Martín Vasques de Arce – Knight of the Order of Santiago – killed by the Moors in relief – the very illustrious Lord Duke of Infantado his lord – to certain people from Jaén to the Acequia – Gorda in the fertile plain of Granada – charged in the hour his body Fernando de Arce his father – and buried in this his chapel – year MCCCCLXXXVI.

[34] This ambulatory has some half-barrel vaults, with transverse circular arches of the nave, one of the chapels that existed in the 12th century, that of Saint John the Baptist and whose entrance was walled off by the mausoleum of Bishop Fadrique.

[21] It is covered with a hemispherical dome on pendentives, which support a majestic roof lantern with the image of the Eternal Father, work of Martín de Vandoma.

[21] The initial part of the chancel, is square and covered with a sexpartite vault, leaves room for four ogee-shaped windows, on the facades north and south.

It had the primitive choir of alabaster attached to its walls and presided over by the chair of the bishop, until in the 16th century it was moved to the center of the main nave after the crossing and in 1491 the Cardinal Mendoza had a new wooden one built.

On the right wall of the Epistle, on the door that leads to the ambulatory, there is the Gothic-Burgundian burial, of the bishop Alfonso Carrillo de Albornoz, cardinal of San Eustaquio, (1424–1434); was commissioned by his nephew the bishop Alfonso Carrillo de Acuña, is the recumbent figure treated with great realism, and is held as an example of Castilian Gothic funerary sculpture of the 15th century, at its sides are the statues of St. Peter and St. Paul and above these some pinnacles ending in a row of blind arcades the sepulcher is inside an ogee[44] Among others is also the sepulcher of Bishop Peter of Leucate, first builder of the cathedral, although the recumbent image was made, later, by order of Cardinal Mendoza, with pontifical dress, mitre and crosier, therefore with vestments after his death.

There are two grandstands, where the Churrigueresque organ is located, with a Plateresque balustrade and shields of the cathedral chapter and the commanding bishop Fadrique de Portugal.

Next to the reredos dedicated to Our Lady of the Snows of 1718, is the sepulcher of Pedro García de la Cornudilla of 1462, the figure of the recumbent is five feet eight inches tall, his head is missing and he is very deteriorated the rest of the monument.

The cloister is attached to the north wall in the central part of the cathedral building, has a square plan with a measure of forty meters per side, these galleries have each of them seven ogival large windows with Gothic drafts all these arcades are protected by iron gates of the same period.

In all its walls it has several graves, as was normal to do at the time: ... next to "de los Caballeros" was given land to the sons of the church, noble and gentlemen; on the north side or «San Sebastián», the relatives of the canonges and beneficiaries were buried; the one of the west or "del Palacio" gave burial to the mortal remains of relative far from the capitulars; the one of noon or of "Santa Magdalena", served as grave to the raoneros canongen and squires.

It is of Late Gothic style, with Renaissance elements, the vaults of the galleries are of sexpartite cross with the keystone in polychrome representing the shields of the cathedral chapter and the bishop López de Carvajal.

There are shields of the bishop placed near the arch of the entrance with an inscription that says: "The protonotary D. Diego Serrano, Abbot of Santa Coloma, founder of this chapel, died on the fourteenth day of the month of March of 1522 years.

The bishop Andrés Bravo de Salamanca (1662–1668) commissioned sixteen tapestries for the cathedral treasury from the Brussels workshops of Jean Le Clerc and Daniel Eggermans.