The monastery was built from 992, outside the walls of Girona, when Ramon Borrell, count of Barcelona gave to the monks rights over the quarter of Sant Pere. The monks held the ruler of the quarter until 1339, when King Peter IV of Aragon restored it to Aragon.

In 1117 Ramon Berenguer III of Barcelona united the monastery to the Abbey of Sainte-Marie de Lagrasse, in what is now France, though Sant Pere kept an abbot of his own and a large degree of autonomy. Sant Pere was never a big community, and the church was not the local parish, and only baptisms were held in the monastery. In 1362, when the monastery was enclosed within the city's walls, it was redesigned to a more defensive shape. It started to decay from the 15th century, and in 1592 it was united to the also decaying monasteries of Sant Miquel de Cruïlles and Sant Miquel de Fluvià. In 1835 the monastery included an abbot and four monks. It was declared a national monument in 1931.

The small cloister is an example of Catalan Romanesque architecture. The northern gallery dates to 1154, while the remaining ones are from 1190. The capitals of the columns have motifs very similar to those in the cloisters of Sant Cugat del Vallès or in the Cathedral of Girona. Some depict scenes from Jesus' life, while others show typical Romanesque elements such as lions or sirens.

 Detail of a capital in the cloister.