In October 1033, King Sancho III of Pamplona gave the monastery to the Abbey of Cluny, by which it became a part of the largest monastic organization of the era.
In 1506 the monastery joined the Benedictine Congregation of Valladolid, which had a program of a return to the reformation of the monastic life, following a strict interpretation of the Rule of Saint Benedict.
In 2012, the foundation Las Edades del Hombre (The Ages of Humankind) held its annual art exhibit in the church of the former monastery.
It was renovated in the 15th century and contains a number of paintings attributed to a monk of the community, Dom Alonso of Zamora.
The Monastery of San Salvador became the final resting place for many of the leading figures of northern Spain, especially during its early centuries of operation.