In the year 1600, Jesuit Missionaries from Punnaikayal took a significant step towards spreading Christianity in the region. They established churches at Thirukazhoor and Srivaikundam, with the latter’s church being blessed on the 24th of July, 1600, by the Jesuit Provincial, Rev. Fr. Nicholas Pimenta. Initially, the church was small, yet it had an enduring legacy. The original structure was designed in the shape of the cross, with a large stone cross placed beside the altar. This distinctive feature earned the church the affectionate name “Cruz Koil,” translating to the “Church of the Cross.” 

Notably, Srivaikundam Church was the first church in the interior region to be built in this cross-shaped design, setting a precedent for later ecclesiastical constructions

In 1644, Srivaikundam was established as a substation of Thirukazhoor, which was the central hub for missionary activities in the area at the time. However, the fate of the church took a turn in 1774, when the Jesuit Congregation was banned globally. During this challenging period, Srivaikundam was placed under the Diocese of Cochin, where it was cared for by Kathimars of the Syrian Rite, as well as priests from Goa.

With the eventual lifting of the ban on the Jesuits, the Madurai Mission was entrusted to the Jesuits of the Thulus Province in France, marking the return of active missionary work in the region.