In 1516, Manuel ordered the publication of a compromise with the "Santa Irmandade da Misericórdia" for the building of the church. At the time, the building was carved into stone with a vaulted ceiling decorated with regal and sacred emblems and supported by marble pillars, dividing the structure into three naves. The presbytery was located in the east, in line with tthe main portico (from plans and sketches dating from the 1755 earthquake). In the south was a door, flanked by sculpted pilasters and three windows (one on the left and the others on the right). The cornice was surmounted by a larger lintel, and on either side was a tower (the western one called "Escrivaninha"), all of which was detailed in the "gravura de Leyden" ("Leyden etchings"). Erected alongside the building was the "Casa da Misericórdia", centre of the local hospital, orphanage, registry, house of the dispatch, offices and courtyard.