I'm not the biggest fan of imperial atrocity competition--it's not like the (for example) Mexican Inquisition was the kinder, cuddlier inquisition. But there's no doubt that the Portuguese saw the cosmopolitanism of India as a major threat to their economic and religious ambitions, and reacted with sometimes stunning levels of violence.

The Portuguese push to round the Cape of Good Hope was an attempted end-run around Muslims' domination of Anatolia and the Near East. They were not too happy, you can imagine, to discover that the eastern African coastline south of Ethiopia was controlled by the powerful Islamic Swahili city-states; nor were they pleased to find Muslims along with "pagans" (Hindus) and Thomas Christians in India and offshore islands. It's become more popular in recent scholarship to talk about 16th century Iberian imperialism as a type of crusade, and India is no exception. The sort of apocalyptic Christian utopianism united with imperial economic-political ambitions had devastating effects in India, particularly the colonial core in Goa.

Afonso de Albuquerque, who led the European conquest and installed himself as the first Duke of Goa, pretty much broke in his office by slaughtering all the Muslim men he could find. As for the women? Well, Muslim and Hindu women alike, the Portuguese decreed, would be married off to incoming Portuguese men to help secure their conversions to Christianity and produce a next generation of native Indian Christians.

The next decades saw waves of mass conversion or "conversion" through public ritual, mob persuasion, basically making Christianity the best option for people. Or the only option: there was a massive campaign of Hindu iconoclasm by European Christians, destroying countless temples and shrines. A good number of churches were built either on top of or out of the rubble of former temples and mosques.

Goa suffered even more than other areas of India. One of the patterns that Ines Zupanov and other scholars of Jesuit/Catholic missionary activity have pointed out is that the further away from a center of imperial political control, the more tolerant or flexible missionaries tended to be. Goa was Portuguese ground zero, and members of European religious orders (think Franciscans, rather than your average parish priest) kept it under tight lockdown. Even with the establishment of a seminary to train and ordain Indian priests, the Europeans locked them out of any position that might earn them a living or any sort of political/spiritual power.

With all of this background, you, gentle reader, probably were expecting the Goa Inquisition, and sure enough it was called and then legislated into being on the advice of Saint Francis Xavier in 1560. Both the delay and the formation of the inquisitorial office had the same reason. By that point, the number of Indian Christians and "New Christian" (conversos or from converso families, that is, Iberian Jews who had forcibly converted to Christianity) immigrants had reached a density to trigger the Catholic religious orders' (Franciscans especially) and secular leaders' paranoia that they weren't actually Christian. The Goa Inquisition investigated tens of thousands of Indians and put over 16,000 of them on trial. Most of the Inquisition records were destroyed in the 19th century. There is mention of around 4200 who were punished in some way; 57 of them were burned alive.

The Portuguese attempt to Christianize its territory in India, overall, has very little to recommend it to posterity.