The interior was also altered during the baroque era. In one of the chapels there is a magnificent silver altarpiece, built in the second half of the 17th century by Portuguese artists. Also in the 17th century the romanesque apse (which had an ambulatory) was torn down and a new one was built in baroque style, later decorated with new wall paintings by Nasoni and choir stalls. The altarpiece of the chapel, designed by Santos Pacheco
and executed by Miguel Francisco da Silva
between 1727 and 1729, is an important work of Portuguese Baroque.
The three red marble holy-water fonts, supported by a statue, date from the 17th century. The baptistery contains a bronze bas-relief by António Teixeira Lopes, depicting the baptism of Christ by John the Baptist.
The South transept arm gives access to the Gothic cloister, which is decorated with baroque azulejos by Valentim
Almeida (between 1729 and 1731). They depict the life of the Virgin Mary and Ovid's Metamorphoses
. The remains of the Early-Romanesque ambulatory contain a few sarcophagi. The terrace is decorated with tile panels by António Vidal. The coffered ceiling of the chapter house was painted with allegories of moral values by Pachini in 1737.
The Se Cathedral is the most commonly used starting point for the Camino de Santiogo on the Portuguese way. Inside the cloister building one can find a statue of Saint James. Outside one can find the yellow arrows leading to Santiago de Compostela and the blue arrows leading to Fatima.