According to a local belief, the church was founded on or before the 4th century by a few Syrian Christian families who had migrated from Paravur and Angamali.

The new church was established in 1338 AD by four Syrian Christian merchants who bought the entire land of Kothamangalam from a local chief for commodity trading with the nearby state of Tamil Nadu.

Present Kothamangalam region was historically known as Malakhachira (മാലാഖച്ചിറ, which literally means "Place of the Angel").

According to tradition, the Apostle, during his mission in India, stayed in this region where he had a vision of archangel Gabriel who instructed him to establish seven and a half churches in Malankara.

A small portion of the Holy Girdle of Saint Mary, rediscovered at the Syriac Orthodox Church at Homs in 1953 by Patriarch of Antioch Ignatius Aphrem I Barsoum, was established in this church In 1980 by the diocesan Metropolitan Thomas Mor Dionysius.