Muslim Tipu Sultan, the ruler of the Kingdom of Mysore, took action against the Mangalorean Catholic community from Mangalore and the South Canara district on the southwestern coast of India. Tipu was widely reputed to be anti-Christian. He took Mangalorean Catholics into captivity at Seringapatam on 24 February 1784 and released them on 4 May 1799.[131]

Soon after the Treaty of Mangalore in 1784, Tipu gained control of Canara.[132] He issued orders to seize the Christians in Canara, confiscate their estates,[133] and deport them to Seringapatam, the capital of his empire, through the Jamalabad fort route.[134] There were no priests among the captives. Together with Fr. Miranda, all the 21 arrested priests were issued orders of expulsion to Goa, fined Rs 2 lakhs, and threatened death by hanging if they ever returned.[citation needed] Tipu ordered the destruction of 27 Catholic churches.

According to Thomas Munro, a Scottish soldier and the first collector of Canara, around 60,000 of them,[135] nearly 92 percent of the entire Mangalorean Catholic community, were captured. 7,000 escaped. Observer Francis Buchanan reports that 70,000 were captured, from a population of 80,000, with 10,000 escaping. They were forced to climb nearly 4,000 feet (1,200 m) through the jungles of the Western Ghat mountain ranges. It was 210 miles (340 km) from Mangalore to Seringapatam, and the journey took six weeks. According to British Government records, 20,000  of them died on the march to Seringapatam. According to James Scurry, a British officer, who was held captive along with Mangalorean Catholics, 30,000 of them were forcibly converted to Islam. The young women and girls were forcibly made wives of the Muslims living there and later distributed and sold in prostitution.[136] The young men who offered resistance were disfigured by cutting their noses, upper lips, and ears.[137] According to Mr. Silva of Gangolim, a survivor of the captivity, if a person who had escaped from Seringapatam was found, the punishment under the orders of Tipu was the cutting off of the ears, nose, the feet and one hand.[138]

The Archbishop of Goa wrote in 1800, "It is notoriously known in all Asia and all other parts of the globe of the oppression and sufferings experienced by the Christians in the Dominion of the King of Kanara, during the usurpation of that country by Tipu Sultan from an implacable hatred he had against them who professed Christianity."

Tipu Sultan's invasion of the Malabar Coast had an adverse impact on the Saint Thomas Christian community of the Malabar coast. Many churches in Malabar and Cochin were damaged. The old Syrian Nasrani seminary at Angamaly which had been the center of Catholic religious education for several centuries was razed to the ground by Tipu's soldiers. Many centuries-old religious manuscripts were lost forever. The church was later relocated to Kottayam where it still exists to this date. The Mor Sabor church at Akaparambu and the Martha Mariam Church attached to the seminary were destroyed as well. Tipu's army set fire to the church at Palayoor and attacked the Ollur Church in 1790. Furthernmore, the Arthat church and the Ambazhakkad seminary was also destroyed. Over the course of this invasion, many Saint Thomas Christians were killed or forcibly converted to Islam. Most of the coconut, arecanut, pepper and cashew plantations held by the Saint Thomas Christian farmers were also indiscriminately destroyed by the invading army. As a result, when Tipu's army invaded Guruvayur and adjacent areas, the Syrian Christian community fled Calicut and small towns like Arthat to new centres like Kunnamkulam, Chalakudi, Ennakadu, Cheppadu, Kannankode, Mavelikkara, etc. where there were already Christians. They were given refuge by Sakthan Tamburan, the ruler of Cochin and Karthika Thirunal, the ruler of Travancore, who gave them lands, plantations and encouraged their businesses. Colonel Macqulay, the British resident of Travancore also helped them.[139]

Tipu's persecution of Christians also extended to captured British soldiers. For instance, there were a significant amount of forced conversions of British captives between 1780 and 1784. Following their disastrous defeat at the battle of Pollilur, 7,000 British men along with an unknown number of women were held captive by Tipu in the fortress of Seringapatnam. Of these, over 300 were circumcised and given Muslim names and clothes, and several British regimental drummer boys were made to wear ghagra cholis and entertain the court as nautch girls or dancing girls. After the 10-year-long captivity ended, James Scurry, one of those prisoners, recounted that he had forgotten how to sit in a chair and use a knife and fork. His English was broken and stilted, having lost all his vernacular idiom. His skin had darkened to the swarthy complexion of negroes, and moreover, he had developed an aversion to wearing European clothes.[140]

During the surrender of the Mangalore fort which was delivered in an armistice by the British and their subsequent withdrawal, all the Mestiços (Luso-Indians and Anglo-Indians) and remaining non-British foreigners were killed, together with 5,600 Mangalorean Catholics. Those condemned by Tipu Sultan for treachery were hanged instantly, the gibbets being weighed down by the number of bodies they carried. The Netravati River was so putrid with the stench of dying bodies, that the local residents were forced to leave their riverside homes.