Originally built in 1521 by a Portuguese nobleman, Duarte Coelho, the chapel was dedicated to the Virgin Mary and known as Nossa Senhora da Annunciada (Our Lady of the Hill). It was used by the Jesuit priest St. Francis Xavier during his missionary travels, and following his death in 1552, his body was temporarily interred here for nine months before being moved to Goa, India.
When the Dutch captured Melaka in 1641, they renamed the building St. Paul’s Church and used it as their primary place of worship for over a century until Christ Church was completed in 1753. Under British rule, the church was used as a gunpowder magazine, and a lighthouse was later added to the front of the structure. Today, it stands as a central component of Melaka’s UNESCO World Heritage listing, symbolizing the city's complex colonial history under Portuguese, Dutch, and British powers.