The original church was built in the pre-Arab period over the ruins of a temple to the Roman god Mercury. In the 10th century, the kings of León established a community of Benedictine sisters on the site.

Following the conquest of the area by Al-Mansur Ibn Abi Aamir (938–1002), the first church was destroyed and the area devastated. León was repopulated and a new church and monastery established in the 11th century by Alfonso V of León.

Alfonso's daughter, the infanta Sancha of León, married Ferdinand, Count of Castile. Sancha's brother, Bermudo III, declared the war against Castile and Castilian troops, with the help of Navarre, killed the Leonese king, becoming Ferdinand I of León. He and his queen gave the crucifix that bears their name to San Isidoro. The church also benefited from its position on the famous pilgrimage route to Santiago de Compostella. Sculptors, stonemasons and artists from across Europe gathered to work on the monastery.

The church was rebuilt as a basilica and rededicated by Ferdinand I and Sancha in 1063. They renamed it San Isidoro in honor of St. Isidore, whose remains were transported to León.[1][2]

Queen Sancha chose the new monastery as the site of the royal burial chapel. Today eleven kings, numerous queens and many nobles lie interred beneath the polychrome vaults of the medieval "royal pantheon". In 1063 the relics of Saint Isidore were transferred to the chapel, and a community of canons was established to maintain the monastery and ward the relics. The apse and transept of the building are in the Gothic style, whilst other parts of the building are Romanesque or of the Renaissance period.

In 1072, after the death of Sancho, Urraca of León and Castile summoned Alfonso VI from exile and reinstalled him as king. Together they planned an enlarged basilica, although the contemporary claims about the specifics of this amplification of the basilica may not be accurate.[3]

The basilica is still a collegiate foundation and the canons' office is celebrated each day.