The “Claustro of Silence”, in Manueline style and designed by Marco Pires, was built between 1517 and 1522, over the previous cloister in Romanesque style, where Manueline symbolism stands out on the ceilings – Cross of Christ, the Armillary Sphere, as well as the Coat of Arms of King D. Manuel I, as well as plant symbols. Walking through this magnificent space we find the Jesus chapel, where the Tombs of D. Pedro Soares (Bishop of Guarda) and D. Rodrigo de Carvalho (Bishop of Miranda) are located, as well as some of the original images of the Church's facade – the The rest are found in the other chapels of this cloister.

In the south wing there is the tomb of Infante D. Henrique, son of King D. Sancho I (second king of Portugal) and the tomb of D. Miguel Salomão (Bishop of Coimbra), above this there is still the tombstone of the consecration of the Church in 1228.
Also noteworthy is the tile paneling that runs through the galleries of the cloister dating from the end of the 18th century – the themes that feature them project religious iconography taken from the Gospels, portraying the Beatitudes and the Parables of Christ's preaching.

In the Cloister there are 3 bas-relief panels, by Nicolau de Chanterene, representing “The Calvary”, “The Descent from the Cross” and “Ecce Homo”.
In this magnificent Cloister there are two fountains:

In the central plane of the cloister, there is a beautiful Fountain dating from 1638 and which replaced the previous ones, with its top topped by the figure of Saint Michael holding the National Shield;

In the southwest angle is the Paio Guterres Fountain, dating from around 1520 (Paio Guterres was a medieval knight linked to the formation of the kingdom, D. Afonso Henriques and the Religious houses of Saint Augustine). This fountain served the refectory ordered to be built by D. Manuel I, and was full of symbolic meaning.

​As we can see, this grand cloister was, over the centuries, readapted to the circumstances and needs of cultural and even political strategies, yet the Cloister of Silence, which we see today, preserves all its beauty and magnificence.