The church of San Juan Bautista is the seat of the parish of San Juan y San Pedro and is one of the oldest in Jaén.

In this temple is the canonical seat of the Real e Insigne Congregación del Santo Sepulcro y de Siervos de la Orden Tercera de Nuestra Señora de los Dolores, which makes its penitence station on Good Friday of the Holy Week of Jaén, and of the Primitiva, Muy Ilustre y Real Cofradía de Nuestra Señora del Carmen, as well as, of the parish groups of the Santísima Trinidad and the Obra Pía de Nuestra Señora del Tránsito.

The temple was built in the second half of the 11th century over an old mosque, proof of which is the existence of the remains of a Muslim minaret in Martínez Molina street, behind the temple.

At the end of the 18th century, the remains of a Roman cemetery were found in its crypt, which means that one of the gates of the Roman wall was there, as these fortifications had four gates and a cemetery on the outskirts of each one. The other two found are located, one near the Puerta del Sol, and the other near the Puerta de Martos.

According to the census of 1595, 606 houses with a total of 2908 parishioners belonged to it. At present its pastoral jurisdiction extends over a population of approximately 4000 people.

Inside, the main altar was presided over by an altarpiece very similar to those designed for the cathedral chapels by the architects Manuel Martín Rodríguez and Gregorio Manuel López, which featured the images of Saint John the Baptist and Saint John the Evangelist, and was crowned with a canvas of the Holy Communion. The walls of the presbytery were decorated with eleven paintings of various themes. The patronage of this chapel was held by the Coello de Portugal family.

To the left of the main altar there was a large chapel ceded in 1695 and rebuilt in 1726 by Juan Manuel de Bonilla y Olivares, in which the devotion of the faithful was offered to the Congregation of the Holy Sepulchre, with the Virgin of Sorrows occupying the chapel. On the other side was a gilded altarpiece with an image of San Jacinto crowned with a silver diadem, flanked by two images of the Child Jesus and the Immaculate Conception.

In the body of the church there were several altars of great devotion, such as those of San Antón, San Félix de Valois, San Juan de Mata, Nuestra Señora de la Encarnación or San Sebastián, as well as a canvas of Ánimas. The choir had a large organ with a horizontal trumpet, the sacristy had beautiful walnut chests of drawers containing a Saint Christ with an incarnated canopy and some paintings, including one of the Transfiguration, Saint James and Saint John the Baptist. Attached to the church was a room used for meetings and assemblies by the Venerable University of Priors, a corporate institution whose statutes were approved in February 1400 and renewed in 1705.

The room had a table and seven walnut seats and was presided over by a canvas of the Crucified Christ, on either side of which hung two others of Saint Nicholas and All Saints. There was also a walnut chest for storing the treasures and a pine cupboard where the very rich archive of the University, now part of the Diocesan Historical Archive, was stored.

In the parochial arrangement carried out in June 1843, which left the capital with only five parishes, that of San Juan was suppressed, leaving the temple as an auxiliary church of the parish of San Pedro and the worship attended by one of its curates.

The main façade, which is quite irregular, is not the original one, which was destroyed in a fire in the 18th century, and of which only a large pointed arch and a belfry on the left angle with remains of Elizabethan Gothic mouldings remain.

Due to its precarious construction, the steep slope on which it stands and the abandonment by the city, the building was left in ruins during the years 1940-1950, which led, drastically, to demolish the interior of the temple, leaving only the perimeter walls standing and configuring a new architectural space, where the antiquity of the exterior contrasts with the functional modernity of the interior.

It is believed that both this church, as well as the square of San Juan and the adjacent streets, were steeply sloping open fields and orchards that were outside the limits of the old Ibero-Roman city and that the buildings that appear at the end of the 11th century are nothing more than the urban expansion that the city underwent at this time.

The interior is very functional, with no remains of the ancient construction. The images of the sculptural group of the Calvary stand out, located in the presbytery behind the main altar. It is dated from the 16th century, of immeasurable artistic value, attributed to Sebastián de Solís, consisting of Christ dead on the cross, on both sides the good thief, San Dimas, and the bad thief Gestas, and at his feet the apostle San Juan, and which are exhibited in the presbytery of the temple together with María Santísima del Silencio, attributed to José de Medina, from the mid 18th century and donated by the Counts of Humanes in 1966. On the main altar there are some polychrome panels belonging to the missing baptismal font from the 17th or 18th century, which is currently being restored.

There is also the carving of Nuestra Señora de los Dolores, also by Sebastián de Solís in 1579, popularly known for being one of the most beautiful sorrows of the Holy Week in Jaén; A sculpture of the Virgen del Carmen, dating from 1949, since the primitive image was barbarously destroyed in 1936, as a consequence of the Spanish Civil War, and its author José Navas-Parejo, whose main festivity is on 16th July, with the imposition of scapulars and a procession; and an image of the Dormition of the Virgin.