The monastery dates back to the Visigothic period of the 7th century. In the 10th century, the abbey was called San Sebastián de Silos, but acquired its current name when Dominic of Silos was entrusted to renovate the abbey by Fernando the Great, King of Castile and León. Dominic had been prior of the Monasteries of San Millán de la Cogolla before being driven out with two of his fellow monks by King García Sánchez III of Navarre, for opposing the king's intention to annex the monastery's lands.