The church’s history dates back to 1503. It owes its origin to the Portuguese Franciscan Friars, who reached Kochi along with Pedro Alvarez Cabral. The church, made of wood and mud, was situated in the middle of the fort that had been constructed by the Portuguese with the permission of the erstwhile Cochin Raja and it was dedicated to St Bartholomew. The church was reconstructed and reopened in 1516 and dedicated to the patron saint of Portugal, Santo Antonio, hence named Santo Antonio Church.The church witnessed various European invasions and during the Dutch invasion of Kochi in 1663, it came under their possession. They converted it into their church by placing their communion table and rostrum furniture. They also constructed a Dutch cemetery adjacent to the church. In 1804, the Dutch surrendered the church to the Anglican Church following the British invasion of Kochi in 1795.  The church was renamed and renovated in 1886. The Church of South India (CSI) took over the administration and management of the church in 1949.