The monastery was founded bottom Maura Dias in 1280 for nuns klarissok. The monastery did not last long, and in 1311 it ceased to exist. In 1316 the wife of King Dinis I, Queen Isabella of Portugal, the restored monastery.

Queen Isabella of Portugal also called "Holy Queen" because of her exceptional piety and righteousness. The Queen also famous for their good character is based hospitals, orphanages and schools. After the death of her husband, King Dinis, she retired to the monastery. And in 1336 the queen died and was buried in the monastery in the tomb, decorated in the Gothic style. In 1626, Queen Isabella was canonized for his charity and good deeds.

The first architect of the monastery was Domingos Domingues, known for his work on the galleries of the monastery of Alcobaça. He continued the work of this architect Estevao Domingues, who was famous for his work on the galleries cathedral in Lisbon. In 1330 the consecration of the temple, and later to the southern part of the church was built a monastery. The monastery is very often presented cash donations and gifts. At the beginning of the XVI century, the church was decorated with Sevillian tiles and installed new altars.

Since the monastery and church were built on the left bank of the river Mondego, then a year later the building was flooded over the banks of the river waters. And for centuries the monastery flooded many times. Due to the frequent floods in the monastery it was not possible to be, and King John IV ordered to leave the building and move to a new monastery - Monastery of Santa Clara-a-Nova, built on a hill not far from the old building. The tomb with remains of Queen Isabella and other royal persons were transferred to the new building.

Over time, the old monastery in ruins. In 1910 the building was listed as a monument of national importance, and some reconstruction works were carried out in the first half of the twentieth century.