The current building was erected in 1517 to replace an earlier Gothic church. The author of the project in the Manueline style was probably Francisco de Arruda. The opening to the worship was held in 1537, with the work unfinished. The Manueline period date the general structure of the temple, fortified church of three naves covered with ribbed vault. The narthex entrance under the tower and the lateral portal are also Manueline. The main portal of the narthex, however, has Renaissance character.

In 1570 the church became the seat of the diocese of Elvas, afterwards becoming  the cathedral . In the 17th and 18th centuries were held numerous stylistic changes that have enriched the interior. During the time of bishop D. Lawrence of Lancaster (1759-1780) the Cathedral won several altars in Estremoz marble, like the one of the main chapel held by José Francisco de Abreu. Also at that time the organ was carved with gilt a work assigned to the Italian Pascoal Caetano Lodovini. Noteworthy is also the fitted room, built in the 17th century.

The diocese of Elvas was abolished in 1881, ceasing the modifications in the temple.

During the decade of 2000  it has undergone a major restoration intervention.