Rafael Cotoner, of the Langue of Aragon, Bailiff of Majorca, was raised to high dignity of Grand Master on the death of Annet de Clermont Gessan on the 5th June 1660. The established reputation for bravery, and the religious zeal with which he was imbued, were among the principal merits which secured for Cotoner the much coveted dignity to the detriment of La Hilliére, Prior of Toulouse, for whose election the party of the "flying squadron" had unsuccessfully directed itself.
Throughout the brief period in which Cotoner's rule lasted we find him enjoying a well-deserved popularity, not only for the good administration of his office, but also for his great affability in private life.
Further reinforcements were, through his exertions, sent from Malta to assist the besieged Venetians in Candia, and the brilliant and glorious deeds of the Maltese contingent under the Knights of St. John increased the renown in which they were held throughout Europe. In token of gratitude for this continual help, and a mark of its appreciation of the valour displayed by the Knights throughout the siege of Candia. The Republic of Venice passed an unprecedented decree permitting members of the Order of the Knights of Malta to appear armed within the dominions of the Republic. A privilege never known to have been accorded to any of the subjects of the Republic themselves.
The prolonged war in Candia did not in any way interrupt those successful naval expeditions which, while rendering the flag of the Order a terror to the Infidel, greatly contributed to the prosperity of the island.
It was during the rule of this Grand Master that the magnificent painting of the roof of St. John's Church was begun by the celebrated artist Matthias Preti, known as the Calabrese, and as a recompense for his valuable services he was received into the ranks of the fraternity.
A malignant fever cut short the great projects which this munificent Grand Master had entertained of further securing the protection of the island, and, after lingering nine days, he died on the 10th October 1663, at the age of sixty-three, after a short reign of three years.