On receiving this reply, Bonaparte immediately ordered his fleet to bombard Valletta and, on 11 June, General Louis Baraguey d'Hilliers directed an amphibious operation in which several thousand soldiers landed at seven strategic sites around the island.

Approximately 2,000 native Maltese militia resisted for 24 hours, retreating to Valletta once the city of Mdina fell to General Claude-Henri Belgrand de Vaubois.

Although Valletta was strong enough to hold out against a lengthy siege, Bonaparte negotiated a surrender with Hompesch, who agreed to turn Malta and all of its resources over to the French in exchange for estates and pensions in France for himself and his knights.

Bonaparte then established a French garrison on the islands, leaving 4,000 men under Vaubois while he and the rest of the expeditionary force sailed eastwards for Alexandria on 19 June.

Political prisoners including Mikiel Anton Vassalli and those who took part in the Rising of the Priests were released, while the Jewish population was given permission to build a synagogue.

[8] The French rapidly dismantled the institutions of the Knights of St. John, including the Roman Catholic Church, and the Maltese people were not happy about this.

There were economic problems and the French government did not pay wages or pensions anymore, and began taking gold and silver from banks and palaces of the Order.

Church property was looted and seized to pay for the expedition to Egypt, an act that generated considerable anger among the deeply religious Maltese population.

On 2 September, this anger erupted in a popular uprising during an auction of church property, and within days thousands of Maltese irregulars had driven the French garrison into Valletta and the Harbour area.