The Portuguese who arrived by sea in 1498, gradually established their power base and were eager to bring all Christians in the fold of the Church of Rome. the Roman Catholic missionaries started to arrive in India with them. The Portuguese tried to introduce the Roman Catholics faith on Thomas Christians / Malankara Christians. With their superior organizational skill and with the help of Portuguese political power Bishop Alexis De Menezes succeeded in establishing the Roman Catholic Church as the dominant Church of Kerala between 1600 to 1650. The Portuguese made an effort to convert local inhabitants to the Roman Catholic faith and also bring some of the existing members of the Syrian Christian Church under Roman Catholic influence. In their combined zeal to colonize and proselytize, the Portuguese might not have readily grasped the way of life of the Thomas Christians who seemed to accommodate differing strands of Eastern Christian thought and influence, while preserving the core of their original faith. The response of the visitors was to try and bring under Romo-Syrian prelates, apart from the new converts in the coastal areas under Latin prelates.

 A Synod ( AD 1599 ) at Diamper ( Udayamperoor ) was conducted under the leadership of Alexisis Menezes, who read the agenda and without any further discussion stated that all points were accepted by the Synod. This was an attempt to diminish the power of Malankara Metropolitan / Archdeacon but the majority of people revolted, pushed beyond a limit, the main body of Thomas Christians rose in revolt and took a collective oath at the Coonen Kurissu ( slanting Cross) in Mattancherry in 1653, resolving to preserve the faith and autonomy of their Church and to elect its head. This event is popularly known as' Coonan Kurissu Satyam' (Oath taken on a bent cross). The immediate provocation was the alleged murder by Portuguese authorities, of a Bishop who was sent from Syria. Accordingly, Archdeacon Thomas was raised to the title of Mar Thoma, the first in the long line up to Mar Thoma IX till 1816. The Portuguese power declined by the 17th century. That weakened the influence of the Roman Catholic Church in Kerala. At the request of the Malankara Christians, the Jacobite Bishop of Jerusalem, Mar Gregorios, came to India in 1664, confirmed Episcopal consecration of Mar Thoma I as the head of the Orthodox Church in India. Those who supported the Roman Catholic Church and its faith, are presently known as Syro-Malabar Christians under the Roman Pope.

 Now Rome entered the field directly through Missionaries, and a section of those who rebelled went back to Roman allegiance.

Vast majority of Malankara Christians, led by the Archdeacon, who stood for the administrative autonomy of the Indian Church in-spite 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 section in the Church to the Roman Catholic community, an equally important section did not follow their way.

 After the decline of the Portuguese the next major influence sprung from British rule. There was a significant influence in the area of education through the efforts of the Christian missionaries which account for the high literacy rate and high degree of education among Keralites.