Having correctly calculated that the Turks would seek to secure a disembarkation point for their fleet and would thus begin the campaign by attempting to capture Fort St Elmo, de Valette sent reinforcements and concentrated half of his heavy artillery within the fort.
His intent was for them to hold out for a relief promised by Don Garcia, Viceroy of Sicily. The unremitting bombardment of the fort from three dozen guns on the higher ground of Mt. Sciberras began on 27 May, and reduced the fort to rubble within a week, but de Valette evacuated the wounded nightly and resupplied the fort from across the harbour. After arriving in May, Dragut set up new batteries to imperil the ferry lifeline. On 3 June, a party of Janissaries managed to seize the fort’s ravelin and ditch.
Still, by 8 June, the Knights sent a message to the Grand Master that the Fort could no longer be held but were rebuffed with messages that St Elmo must hold until the reinforcements arrived.
Finally, on 23 June, the Turks seized what was left of Fort St. Elmo.
They killed all the defenders, totaling over 1,500 men, but spared nine Knights whom the Corsairs had captured, and a few others managed to escape. Balbi writes that Dragut died shortly after the victory. According to Bosio, a lucky shot from Fort St. Angelo mortally wounded him on 18 June; whereas according to Balbi and Sans, friendly fire from Turkish cannons while he was directing operations on Sciberras was the cause.
Although the Turks did succeed in capturing St. Elmo, allowing Piyale to anchor his fleet in Marsamxett, the siege of Fort St. Elmo had cost the Turks at least 6,000 men, including half of their Janissaries.
Mustafa had the bodies of the knights decapitated and their bodies floated across the bay on mock crucifixes. In response, de Valette beheaded all his Turkish prisoners, loaded their heads into his cannons and fired them into the Turkish camp.
“If the Turks should prevail against the Isle of Malta, it is uncertain what further peril might follow to the rest of Christendom” – Queen Elizabeth I of England