The true origin of the monastery is not known, which has given rise to speculation and legend; such as its foundation by monks who disembarked in the area with the remains of Saint Peter and other saints, to save them from the "Barbarian hordes" that were invading the Western Roman Empire. Once the danger had passed, the Pope Boniface IV commanded them to build a monastery.

The first documentation of the existence of the monastery dates 878, when it was mentioned as a simple monastery cell consecrated to Saint Peter, but it is not until 945 when an independent Benedictine monastery was founded, led by an abbot. Connected with the County of Empúries, it reached its maximum splendor between the 11th and 12th centuries until its final decay in the 17th century. Its increasing importance is reflected in its status as a point of pilgrimage.

In the 17th century it was sacked on several occasions and in 1793 was deserted by the Benedictine community, which was transferred to Vila-sacra and finally settled in Figueres in 1809, until the monastery community was dissolved.

The monastery was declared a national monument in 1930. In 1935 the first restoration work was initiated.