In 52 AD, St. Thomas, the apostle landed in India at Maliankara near the port of Muziris. This Port was also called Muchiri because the River Periyar's branches out into three (In [Malayalam] these three branches were called Muchiri or three broken lips) before it joins the Arabian Sea. This was one of the oldest and busiest port on the West Coast of India known to the world by more than twenty different names. In the biggest ever flood known in the history of Kerala, this Port was washed off in 1341 AD and a new Island known as Vypin was formed near Kochi or Cochin in the Vembanad Lake. People from various places migrated to the new island.
The Portuguese built a fort at Pallipuram as a watchtower in 1503. It is the oldest existing European fort in India. At the same time, the Portuguese built a church for the believers of the surrounding area and dedicated it to Our Lady. It was the church at that time where Christians in that area gathered together for worship.
During the Mysorean invasion of Kerala in the 18th century, Tipu Sultan was camped near the River Chalakkudy in order to attack parts of Travancore. He destroyed most of the Christian and Hindu places of worship. The local people gathered together in the church and prayed to Our Lady for her help. At that time, there was a mist (snow) spread around the church and Tipu and his military could not see the church or the surrounding areas. They thought it was part of the Arabian Sea. There was also a high flood in the River Periyar and Tipu lost a huge part of his military and returned to Mysore. It was the miracle that changed the name of Our Lady to Manjumatha (Our Lady of Snow).
In 2007, the Church celebrated its 500th anniversary.
The church was renovated in 1931 and 2006.