This was the first church built in Valletta. It was built on the spot where a religious ceremony was held to inaugurate the laying of the foundation stone of the new city on 28th March 1566, and commemorates the victory over the Turks during the so-called 'Great Siege' of 1565.
Grand Master La Valette was originally buried here, and his remains were later transferred to St John's Co-Cathedral. In 1617 it became the Parish Church of the Order.
Changes were made in 1752 and the facade, the sacristy, the belfry and the parish priest's house were enlarged. The church originally had two altars - one dedicated to St John the Baptist and the other to St Paul. Two other altars were built during the latter part of the eighteenth century.
The church suffered a lot of deterioration over the years, both to its structure and to the paintings which include works by Francesco Zahra, Ermenegildo Grech and Enrico Arnaux. In 2000 a joint project was set up between Din l-Art Helwa, the Valletta Rehabilitation Project and the Museums Department to carry out restoration work on the structure and the paintings. Shortly afterwards restoration was carried out on the roof, finials and part of the belfry, which was sponsored by Computime. The restoration of the external structure was completed in 2004 thanks to a major sponsorship by PricewaterhouseCoopers.