This temple has a Mannerist frontispiece and a galilee entrance from 1709. It has three naves, with the main chapel and a gilded altarpiece, with blue and white tiles showing scenes of St. Francis of Assisi on the walls and a magnificent group of chairs made of exotic wood. In the side chapels, as well as in their altars, there are magnificent pieces of sacred art, among them images of Saints dating from the 17th and 18th centuries.
The ceiling of the three naves is ornamented with paintings alluding to religious themes. In the high choir, there is an organ of tubes dating from the eighteenth century, which is the largest of the whole city and even the island of São Miguel. Annually, in this church several concerts of classical music take place, promoted and organized by the São José Choir (founded in 1967).
The Sacristy is located behind the main chapel, at the top of the church, where there is a rich exotic wood arcade with paintings on canvas depicting the life of St. Francis of Assisi, as well as the oil-painted ceiling on wood with flower motifs and figures connected to the Divine. Also, there is a fountain with two spouts and a basin built of volcanic stone.