The Museum, which consists of the treasury and catacombs, is located in the building adjacent to the church. Catacombal Cemetery is a private cemetery, built in 1746-49, and before 1866, there were no public cemeteries in Portugal. The Health Law of Costa Cabral Minister cancelled private burials. Lots of black tombs are along the walls, and upstairs is the session room built by Nicolau Nazoni, covered with a paneled, gilded woodwork ceiling by Tinoco. There is also a carved baroque altarpiece. General assemblies of St. Francis's Order are held in this room.

The building of the Church of St. Francis was started in 1245 and finished in 1410. There was also a monastery which was destroyed, and now Palacio da Bolsa is in its place. The church entrance porticos and arches with gilded leaves on the ceiling are Romanesque, covered with baroque gilding. The church naves are Romanesque-Gothic; however, you can barely see any walls or arches at all – the whole church is just baroque gilding, literally top to bottom. On the left, there are several chapels with heavy baroque gilding and baroque paintings -- the most famous of these chapels has the tree of Jesse (1718/19) in it.

The tree is an example of national baroque style in Portugal – rather primitive statues of Jesse’s descendants on the branches of the tree, at the roots of which is Jesse himself. Joanin baroque is presented in the altar and two chapels on its sides –- gold baroque columns with embellished steps underneath a large baldacchine, ending with crucifixion and royal symbols. The light coming through the windows behind the altar is almost blinding you, reflecting from the gilding.

The ceiling has heavily gilded floral designs that continue along the columns and arches and into the high choir above the entrance on the balcony. On the left side, there are several chapels with lots of gilding -- part of this side is rococo after 1750, especially Our Lady of Sorrow Chapel. The organ on the balcony is also rococo, with, once again, lots of gilding. The balcony and high choir cannot be visited. The only genuine Romanesque-Gothic arch left is to the right of the altar, leading to the chapel in the corner. The façade is Romanesque, with baroque columns surrounding the entrance, and both the bell tower and museum building are rococo.