The works sponsored by the Queen started in 1316 on the same spot of the previous foundation and gave rise to the ensemble that exists today. The first architect associated with the monastery was Domingos Domingues, who had worked on the cloisters of the Monastery of Alcobaça. His work was continued after 1326 by Estêvão Domingues, who had worked on the cloisters of Lisbon Cathedral. The church was consecrated in 1330 and shows the influence of the Alcobaça building in its floorplan and many other architectural details. Queen Elizabeth died in 1336 and was buried in the monastery in a magnificent Gothic tomb. A large cloister was built to the South side of the church still in the 14th century.
Already in 1331 the monastery and church were flooded by the Mondego, whose banks are located nearby. The site of the foundation would prove to be inadequate, since the monastery was repeatedly invaded by the waters of the river in the following centuries. The sisters of the monastery responded by elevating the floor levels of the monastic buildings to reduce the damage caused by the floods. In spite of the problems, the monastery was frequently enriched by donations. In the early 1500s, under King Manuel I, the church was decorated with Sevillian tiles and several painted altarpieces.
As the centuries passed, the old monastery fell into ruins and became partially submerged by the mud and water of the Mondego. Its historical and architectural importance led to it being declared a National Monument in 1910, and some conservation works were done in the first half of the 20th century. After 1995, a large archaeological campaign by the Instituto Português do Património Arquitectónico has removed the mud and water from the ruins, which were found to be in a remarkable good state of conservation. The excavations allowed for the recovery of a large number of architectural and decorative fragments and a better understanding of the monastery plan. In 2006 the building of an interpretation centre and new tours were announced. This phase of the project has an estimated cost of 27 M€ and is intended to be completed by 2009 .
The nave used to be divided in two parts, one of public access and the other reserved for the nuns, separated by a dividing wall. An elevated choir, now lost, used to host Queen Elizabeth's tomb. The apse of the church has three chapels of polygonal shape, the central chapel being the largest. The central chapel has lost its stone roof and used to be illuminated by three windows.
A portal on the South façade of the church connects it with the cloister ruins, which have been preserved up to the level of the double columns of the arches. The capitals are decorated with vegetable motifs. Also visible are the remains of a Gothic fountain with a circular basin.
The excavations also revealed the foundations of the chapter house, refectory, a smaller cloister and the old Palace of Queen Elisabeth.
Many works of art of the monastery are now in the Machado de Castro Museum in Coimbra. Painted altarpieces include a triptych of circa 1486 about the life of Claire of Assisi and a painted triptych commissioned to Flemish painter Quentin Metsys in 1517 Others pieces of sculpture and metalwork in the museum testify to the wealth and prestige of the monastery.