The origins of the monastery of Sant Quirze de Colera are unclear. According to a document considered to be false (although not in its entirety), it is possible that around the year 785 several members of the same family, led by the brothers Libuci and Assinari, settled here.

The initiators of the initiative would have taken the lead in founding a monastery on this site with an authorisation granted by Charlemagne. Before the year 815, they obtained a royal decree which already mentioned the monastery and made it the beneficiary of various assets. Despite the unreliability of this information, important architectural elements and tombs from that period have been discovered that prove, at least, its antiquity. That precept of Charlemagne would have been the starting point for a series of donations and foundations of parishes under the direction of the monastery of Sant Quirze. Later, the monastery, which was a private foundation owned by the family of the founders, received from them the ownership of the property. After an attempt of interference by Count Alaric of Empúries, the abbot of Sant Quirze asked Ludovico Pio in 844 to recognise the foundation and the rights acquired.

After a period without news, possibly due to some war incursions, the monastery is already mentioned in a reliable way in 927, in a document where the name of its abbot, Manuel, appears, which marks the beginning of a period of growth. In 935, the bishop of Girona inaugurated the monastic church, built thanks to the financial support of Count Gausbert of Empúries, who benefited Sant Quirze with more properties and rights. In the following years, Colera played a decisive role in various acts related to other monastic centres in the surrounding area. In 1123, Bishop Berenguer of Girona presided over the consecration ceremony of the new church, and at that time the church of Santa Maria was also mentioned. In the following years, important donations continued to be recorded in its favour.

In 1285 and again in 1288, it suffered the effects of the passage of French troops as a result of the conflicts between the armies of Philip the Bold and the Crown of Aragon. In the 15th century, signs of decadence and the existence of commendatory abbots began to appear. There is evidence that in 1441 the cloister was in danger of ruin. In 1592, the monastery was suppressed and the community was extinguished and integrated with that of Sant Pere de Besalú. With the exclaustration of 1835, the assets of the latter monastery were auctioned off and Sant Quirze de Colera passed into the hands of the military and political figure Ramon de Nouvilas. The buildings were used for agricultural purposes and were sometimes abandoned. In 1931 it was declared a National Monument and in recent times excavation, consolidation and restoration works have been carried out.

The most important building in the complex is the church, with three naves and a transept with three apses. There are remains of the cloister, fortified elements, outbuildings surrounding the cloister and the abbot's palace. To the west of the complex is the small Romanesque parish church of Santa Maria.