Sancha Alfónsez of León, daughter of King Alfonso V, became abbess of the Monastery of San Pelayo at a very young age. Together with her husband Fernando, she reigned in León beginning in 1037. Sancha exerted a notable influence on the monarch to promote the construction of the stone church of San Juan Bautista and, furthermore, persuaded him to choose this church as his burial site, ruling out other options he had considered, such as the monasteries of Arlanza or Oña. The project came to fruition with the demolition of the modest church built during the reign of Alfonso V and the construction of a new temple of finely worked ashlar, as recorded in the chronicles of the time. This was not a large church intended for popular worship, but rather a small palatine chapel designed for the private use of Ferdinand and Sancha, who resided in the palace adjacent to the dual monastery, comprising a community of nuns and another of canons.

Likewise, the space designated for the Royal Pantheon was reorganized. This is confirmed by the consecration plaque and recounted by contemporary sources, such as the chronicler known as El Silense, who was also a cleric at San Isidoro. In the cemetery located at the foot of the church—the current Royal Pantheon—the founding monarchs, Ferdinand and Sancha, were buried alongside three of their children: Urraca, Elvira, and García. The cenotaph of García Fernández, the last Count of Castile, is also preserved there. The epitaph of Ferdinand I, who died in 1065, highlights that it was he who transformed a church that had previously been built of humble materials into stone.

In order to ennoble the temple, and following the customary practices of the time, it was considered essential to gather prestigious relics. For this reason, in 1062 the remains of Saint Isidore were transferred from Seville, and from the monastery of Arlanza, the relics of Saint Vincent of Avila, which had been kept there following the raids of Almanzor. Additionally, the church had long preserved a jawbone attributed to Saint John the Baptist.

The new church was solemnly consecrated on December 21, 1063, under the patronage of Saint Isidore. On this occasion, the monarchs endowed the church with a valuable set of liturgical vestments which, from an artistic standpoint, constitutes one of the great treasures of the Romanesque period. From that time on, the building was dedicated exclusively to Saint Isidore.

Ferdinand and Sancha consistently protected the church, visiting it on numerous occasions, as chroniclers recount; they even describe the moving scenes of King Ferdinand I visiting the site in the final moments of his life. The complex was enriched with important relics, pieces of gold and silverwork, and abundant treasures, while the monastery received a substantial endowment.

This church became the first Romanesque building in the Kingdom of León constructed in accordance with the most advanced trends of this style. The building commissioned by Ferdinand I and Sancha was small in size: it measured about 16 meters in length and was organized into three naves, with a central nave three meters wide and side naves about two meters wide. It featured a remarkable height, reaching twelve meters in the central nave and seven in the side naves. The apse was tripartite, with straight and stepped end walls, covered with barrel vaults, and lacked a transept.

At the foot of the church, the royal pantheon was built, which was accessed from inside the temple through a door that is now blocked. According to archaeological excavations, its walls were aligned with those of the naves. It was an enclosed space, organized on two levels: the lower level intended for burials and the upper level designed as a royal tribune.

From this construction phase, the following elements are preserved today: the Royal Pantheon; a doorway with sculpted capitals located on the upper level of the pantheon between the current Archive and the Treasury; the royal tribune; the two attached porticos; the first two sections of the tower; and the north and west walls, which were later incorporated into the expansion promoted by Urraca la Zamorana. In 1908, during restoration work led by the architect and conservator Juan Nepomuceno Torbado, the original floor plan and foundations of this church were uncovered. Decades later, during paving work in 1971, the building’s layout was documented once again; this study was carried out by the German Archaeological Institute in Madrid under the direction of Professor Williams.