Reconstruction took a number of years since various of alterations were introduced,[4] including the replacement of the original interior columns with cylindrical classical ones reflecting contemporary taste (a revival of the style of the second half of the sixteenth century) similar to what occurred in Lagoa and St. Peter (São Pedro) of Faro.

[2] It is thought that, as in Lagoa, the Faro master carver Manuel Francisco Xavier,[7] among others, played a part in the design and supervision of the reconstruction.

[4] An earthquake on 28 February 1969, caused further damage to the towers, vaulted ceiling over the altar, the triumphal archway and divisions between the naves.

[9] The three altars at the chancel-end of the church fit the Baroque style both in their decoration and in terms of the tile facings on the walls.

The tiles covering the vaulted areas around each of the altars and the end wall of the nave above the chancel date to 1719 and reflect the popular national blue-on-white style of the period.

One panel in the chancel represents St. James on a caravel fighting the Moors in the naval Battle of Lepanto (1571) in which Dom John of Austria defeated the Turks.

[13][17] The Chapel of Christ Crucified (Capela do Senhor Jesus Crucificado) was constructed in 1589, according to a date on the front of the arch over it.

The central area is filled by pictures of Our Lady of Sorrows and of St. John the Evangelist, and by the large sculpture of Christ Crucified.

After the arrival of Europeans, ivory carvings of western religion themes were produced in large numbers in the 17th and 18th centuries, mainly for the metropolitan market where they were installed in many private oratories of wealthier people.