Built in 1230, on the site of the main mosque in Elvas, the church has undergone transformations, hiding the Arab remains, which have been disappearing for centuries. The mosque was built in the 8th century and closed after the conquest of the city of Elvas by King D. Sancho II in 1230. From the original mosque, the south-facing mirhab (Mecca) remains, which was locked up, probably during the 16th century. This mirhab exists today as a visible projection on the outside of the church, on the right side, with some battlements on top. Initially of royal patronage, the church was donated to the Order of Avis in 1303, by D. Dinis. It underwent profound changes in the 16th, 17th and 18th centuries, giving it its current appearance.

The facade of the Church of Santa Maria de Alcáçova is simple, with a pietá in the center at the top. The interior has three vaults. The chancel, also of simple style, has a stone image of a 15th century Pietá. One of the two collateral chapels is in masonry from the 18th century, with an image of Our Lady. The second, dedicated to São João Baptista, is built in 17th century gilt carving. The side chapel on the left side was completely covered in gilt carving from the second half of the 17th century. The chapel on the opposite side is in masonry.