The Indian Church came in contact with the East Syrian Church possibly from the 4th century. In the 5th century, the church of Persia came to its own. The Catholicos with his seat at Seleucia -Ctesiphon began to be called also Patriarch and in 486 A. D. the Church officially accepted a resolution in its Synod to recognise Nestorius as a Saint and Church Father. This decision was not however accepted by a minority of Persian Christians who acknowledged a Catholicos at Tagrit in northern Mesopotamia as their spiritual head in 629 A. D.

We have evidence that in the 8th century the Indian Church had its Primate known as "The Metropolitan and the Gate of All India" a title adopted presumably under Islamic influence. The Vatican Codex 22, written in Cranganore in 1301 gives the titles as "The Metropolitan of the Throne of St. Thomas and of the whole Church of the Christians in India."

The Indian Church maintained its autonomous administration. The Church of Persia had a tradition which acknowledged autonomy of Churches in its communion abroad. The Church in Kerala continued as an administratively independent community till the 16th century.