In 1573 Grand Master Jean de la Cassiere authorized the constuction of a conventual church of the Order of St. John. It was completed in 1578 by the Maltese architect Girolamo Cassar. Alessandro Algardi’s bas relief of the Saviour surmounting the façade was relocated here in the 1850s from its original place in a chapel close to the entrance of the Grand Harbour. The spires on the bell towers were destroyed during the Second World War. The rectangular Baroque interior was embellished by successive Grandmasters and further enriched by the “Gioja” or present, which every Knight was bound by statute to give on admission to the Order.

Between 1662-67, Mattia Preti “Il Calabrese” painted the life of St. John the Baptist, patron saint of the Order, directly on to the primed stone of the ceiling. The Cottoner brother paid for this work. In the ornate Oratory is a 3 by 5 metre painting by Caravaggio depicting the beheading of St. John. This painting is regarded as the masterpiece of Caravaggio and is the only one of his paintings which bears his signature.