The current building was erected from 1517 to replace an earlier Gothic church. The author of the Manueline style project was probably Francisco de Arruda. The opening to worship was held in 1537, with the works still unfinished. The general structure of the temple dates from the Manueline era, a three-navy fortress church discovered with a ribbed vault. The entrance narthex under the tower and the side portal are also Manueline. The main portal, by Miguel de Arruda, dates from 1550 and has a Renaissance character.

In 1570 the church became the seat of the diocese of Elvas, thus ascending the cathedral (Sé). In the 17th and 18th centuries, numerous stylistic changes were made that enriched the interior. At the time of Bishop D. Lourenço de Lencastre (1759-1780), in particular, the Cathedral won several marble altars from Estremoz, such as the chancel made by José Francisco de Abreu. Also at that time, the organ's gilt work was carried out, attributed to the Italian Pascoal Caetano Oldovini. Also noteworthy is the cabido room, built in the 17th century.