Things changed during the Portuguese period. The missionaries who came from abroad were eager to bring the Indian Church into communion with Rome. They worked on it almost through the 16th century. In 1599 by the Synod of Diamper, the assembly of representatives from churches was forced to give up the Indian Church's connection with the Patriarch of the Persian Church in favour of the Pope of Rome. But there was dissatisfaction among the people. This dissatisfaction led to a general revolt in 1653 known commonly as the Coonan Cross revolt. Portuguese efforts to put it down by force did not succeed. Now Rome entered the field directly through Missionaries, and a section of those who rebelled went back to Roman allegiance.

A body of the people led by the Archdeacon, who stood for the administrative autonomy of the Indian Church inspite of serious difficulties were determined to keep to the independence of the Indian Church. The Portuguese were in fact instrumental in causing a division in the one united church in India. Although they succeeded in getting the allegiance of a party in the Church to the Roman Catholic community, an equally important party did not follow their way.