The Syrian Christian Church (several denominations were formed since 17th centuary only in Kerala) is believed to have been shifted to Chempu from Kulasekharamangalam, about 1.5 KM south of Chempu as per govt. order on the request of Vaikom Mahadeva Temple authorities. The annual procession of the Temple used to come up to the Church at Kulasekharamangalam, and the Temple authorities wanted to extend their procession up to the border of Kulasekharamangalam. Hence both Church and Mosque were shifted to the present place. The Church at Chempu was constructed in AD 1307 in 24 cents of land allotted by the Govt.

The aftermath of the Udayamperoor Synod held in 1599 reflected in Chempu Church also which finally resulted in the formation of 2 factions – Jacobite and Catholics after (Koonankurizhu Satyam) 1653, However both fractions continued to use the same Church with different timings for a very long period. This arrangement continued until the Church was closed down in 1859 on the instruction of Catholic Bishop of Varappuzha. Holy mass had to be conducted in temporary sheds by both factions.

The rift resulted in several clashes between the factions and legal battles- both civil and criminal continued from 1864 to 1891. Several families have fled from here during this period to far away places like Kottayam, Manarkad, Arpukkara, Ranni, Muvattupuzha, Arakkunnam and Tripunithura. The members of these families regularly visit this Church.

In 1877, as per mutual agreement between the factions, 8 cents of the total 24 was given to Jacobites. The construction of the present was started in 1867. In 1879 some of the families of this church residing at Manakunnam and suburbs constructed a church there about 5 KM S-E from Chempu. And in 1958 a church was constructed at Brahmamangalam for the convenience of the families from that area. At present there are only 104 families at this church, scattered over Chempu Kulasekharamangalam, Udayanapuram, Enadi and Vaikom.