By 1795 the British established themselves in South India and Kerala came under their sway. During the time of Col. Munroe who was the British Resident in Kerala, Pulikottil Ittoop Ramban expressed his interest in founding a Seminary for the teaching of the Church's clergy. The Resident supported him and the seminary was founded in 1815. Pulikottil Ittoop Ramban became a Bishop -Metropolitan Mar Dionysius II.

 When the British became a colonial power in India, the Anglican domination of the Theological Seminary at Kottayam, besides attracting members of the Church into Anglican congregations since 1836.

 From 1816 the experiment of co‑operation between the Malankara Church and the C. M. S. of the Anglican Church was carried on, but it was found to be unsuccessful and was called off in 1836.

 This incident led to the division of the community into three bodies. One of them a reformed group tried to bring about serious reforms in the liturgy and practices of the Church as a whole but failed. After about half a century of conflict within the church this body had to withdraw and organize itself as the Mar Thoma Syrian Church. A smaller body of the Syrian Christians opted to join with the missionaries and be absorbed in the Anglican Church. The majority of the community continued in the Church without accepting the reforms.

 Around 1800 one of the Syrian Christian Bishops, Mathew Athanasius, influenced by one Abraham Malpan made a move to the Protestant side and this was the beginning of the Kerala Mar Thoma Church. The reformist group with newfangled Anglican ideas broke away under the leadership of Palakunnathu Abraham Malpan and his nephew Dn. Mathews, later consecrated as Mathews Athanasios, a bishop of the Church, to form Mar Thoma Church in 1889. They developed strong links to the Western missionaries and emphasized evangelical renewal and Bible study. But the majority of the parent Syrian Church remained loyal to their own Bishops.

 The conflict between the body, which adopted the reform, and that, which opposed it, was a serious development in the church during the 19th century. This led to the latter to appeal for help from the Antiochene Syrian Patriarch. In 1875 Patriarch Peter 111 came to Kerala and held a Synod of representatives of Churches. at Mulanthuruthy in 1876. This Synod adopted a number of resolutions including an admission that the Church would continua in the communion of the Patriarch and the Syrian Church of Antioch. However the Patriarch tried to see in these decisions more than the Indian Church really wanted to acknowledge.

This crisis situation was contained with the help of Patriarch Peter III of Antioch who visited India( 1875-1877 ). The outcome was two fold : a reaffirmation of the distinctive identity and faith of the Orthodox Church under its own Metropolitans and, at some dissonance with this renewal an enlarged influence of Patriarch of Antioch of the Indian Church.

 Following the Synod of Mulanthuruthy in 1876 a litigation in court between the party in favor of the reforms and the party against it continued. It came to an end in 1889 with the judgment announced in favor of 'the latter by the then highest court of Kerala, the Royal Court of Appeal. The majority in a panel of three judges gave their verdict admitting that from the middle of the 18th century an over‑all spiritual supervision used to be exercised by the Patriarch over the Malankara Church and that he had a right to claim it.

 Thus a relationship which started for safe-guarding the integrity and independence of the Orthodox Church in India, against the misguided, if understandable, ambitions of the roman Catholic and Anglican Protestant Churches opened a long and tortuous chapter in which concord and conflict between the Indian and Syrian Orthodox Churches have continued to alternate to this day.