The spiritual and temporal matters of the church were controlled by a few powerful Syrian Christian families for more than a century. Personal differences among some of the influential members of the managing committee over the ‘Pasaram’ due to the church led to the separation of eighteen families who eventually built the historical Mar Thoma Cheriyapally.

In 1455 A.D. Kaimal, the local administrator, allotted land for them at ‘Kollikattumala’ for the construction of a church. They first erected a Cross and worshipped there. This Cross was uprooted and thrown into the river by miscreants. Another Cross was erected in the presence of the Karthas and sweets were offered to those present. A church was built there on Kanni 13. Its thatched roof caught fire and subsequently the roof was tiled.