After a couple of years, the building of the fort and the St. Francis Church were reconstructed by a Portuguese viceroy from wooden building to the stone building. During this process the wooden church was rebuilt and was dedicated to St. Anthony, hence the name St. Anthony church. Kochi is known for having the influence of foreign lands multiple numbers of times from the Portuguese to Dutch to the Britishers.
When the Britishers captured Kochi in the year 1795, the name of the patron was changed from St. Anthony St. Francis and till date, the church is still known as St. Francis Church. This church is now taken over by the state government of Kerala and was declared as a protected monument under the Archaeological Survey of India. Even the remains of Vasco Da Gama were kept in this church when he died during his third visit to Kochi (i.e. in the year 1524) but were later transferred to Lisbon after a couple of years.