The decoration of the barrel vault (named after its rounded ceiling) began in 1660.

Normally, paintings on walls are carried out in a fresco technique which is water colour based, but here Preti used oil based paint and applied it directly onto the stone.  He started from the lunette above the main door where he depicted the allegory of the Order represented by Minerva, the goddess of war and wisdom, crushing Moorish slaves beneath her feet. To the left and right are the Cotoner grandmasters Raphael and Nicolas (who were great benefactors of the Order and this church). On careful inspection, knights can be seen in heaps, slain in battle, and angels descending from the sky holding palm fronds. This is a symbol of martyrdom.

For the next six years Preti toiled with the rest of the vault. He ingeniously used its six bays to fit his narrative cycle. Each bay is subdivided into three sections. The story of St John starts from the first bay at the main door with the vision of the priest Zachary and ends with the beheading of the saint in the 6th and last bay to the right of the altar. In the apse he painted St John holding the Order’s standard, being presented to God the Father by Jesus Christ.