The Portuguese Viceroy Redondo (1561-64) commissioned the Se’ or St Catherines’ Cathedral, southwest of St Cajetan’s, to be " a grandiose church worthy of the wealth, power and fame of the Portuguese who dominated the seas from the Atlantic to the Pacific". Today it stands larger than any church in Portugal, although it was beset by problems, not least a lack of funds and Portugal’s temporary loss of independence to Spain. It took eighty years to build and was not consecrated until 1640.

On the Tuscan-style exterior, the one surviving tower houses the Golden Bell, cast in Cuncolim (south Goa) in the seventeenth century. During the Inquisition, its tolling announced the start of the gruseome auto da fe’s that were held in the square outside.

Reconstruction of parts of the roof, which once had overhanging eaves, has damaged some paintings inside. The scale and detail of the Corinthian-style interior is over-whelming; huge pillars divide the central nave from the side aisles, and no less than fifteen altars are arranged around the walls, dedicated among others to Our Ladies of Hope, Anguish and Three Needs. An altar to St Anne treasures the relics of the Blessed Martyrs of Cuncolim, whose failed mission to convert the Moghul emperor Akbar culminated in their murder by Muslims, while a chapel behind a highly detailed screen holds the Miraculous Cross, which stood in a Goan village until a vision of Christ appeared on it. Said to heal the sick, it is kept in a box; a small opening on the side allows devotees to touch it. The staggeringly ornate gilded main altar comprises nine carved frames and a splendid crucifix. Panels depict episodes from the life of St Catherine of Alexandria (died 307 AD), including an interchange of ideas with the pegan Roman emperor Maxim, who wished to marry her, and her subsequent flogging and martyrdom.