The church and monastery that today make up the Basilica of San Isidoro were founded around the year 956 on a site near the Roman wall of the Legio VII Gemina, in its northwest sector. The western part of the building rests directly on this wall, even overlapping it in places. Numerous sections of the ancient fortification are still preserved in good condition in that area. Furthermore, beneath the premises of the Collegiate Church and following various restoration projects, significant Roman-era remains have been identified, such as solid brick walls, sewer systems, ceramics, roof tiles, and latrine conduits, some of which bear the seal of Legio VII.

No remains corresponding to the Visigothic period or the Muslim rule have been found, nor from the early stages of the Reconquista. The oldest references in chronicles and documents date from the mid-10th century and mention the churches of San Juan and San Pelayo, which began to gain prominence at that time.

It was King Sancho I of León, known as Sancho the Fat, who promoted the construction of this church. Over the centuries, and up to the present day, the complex has undergone profound transformations in both its structure and its spiritual function, experiencing periods of great splendor and others of notable decline. These different historical phases were strongly marked by the influence of the monarchs and their family circles.