A few months after the invasion, discontent due to reforms that were taking place led to an uprising, which evolved into a blockade of the French garrison by Maltese insurgents aided by the British, Neapolitans and Portuguese.

Meanwhile, France and the other major European powers began to take an interest in Malta due to its strategic position in the central Mediterranean and its system of fortifications, which was one of the strongest in Europe.

Maltese soldiers and militia led by members of the Order were responsible for the defence of the fortified cities in the Grand Harbour area: Valletta, Floriana, Birgu, Senglea and Cospicua.

On 9 June, Napoleon sent his aide-de-camp Jean-Andoche Junot to request permission from the Grand Master for the French fleet to water at Malta.

It stated that the French were treating the Order as an enemy, but it promised to respect the religion, customs and property of the Maltese population.

[7] Following the capture of the fort, the defenders abandoned the other coastal fortifications in the bay, and the French landed the bulk of their forces unopposed.

A galley, two galleots and a chaloup of the Order's navy sailed out of the Grand Harbour in an attempt to prevent the landing, but their effort was futile.

At a city council meeting at the Bishop's Palace, it was decided that resistance was futile and they agreed to capitulate if the people's religion, liberty and property would be respected.

[8][10] The French force which landed on the island of Gozo consisted of the 3rd Company of Grenadiers and the 95th Demi-Brigade, and it was led by Jean Reynier.

[11] The landing began at around 13.00 in the area of Redum Kebir (Maltese: Rdum il-Kbir) in the vicinity of Nadur, between the Ramla Right Battery and the Sopu Tower.

[11] Reynier and part of the 95th Demi-Brigade subsequently marched to Fort Chambray which commanded Gozo's main harbour, Mġarr, in an attempt to cut off communication with Malta.

[8] Some pressured Hompesch to negotiate with Napoleon and come to terms of peace,[10] and Maltese representatives petitioned the Grand Master to reach an armistice.

[15][16] The French blockaded Fort Tigné and bombarded it repeatedly on 11 and 12 June, and its defenders were unaware of the negotiations that were taking place at the time.

The Monsieur de Fremaux, the consul of the Batavian Republic, was initially chosen to bear a letter to the French asking for a truce.

Due to Fremaux' old age, Monsieur Mélan, a member of his staff, was sent instead, and he arrived on the French flagship L'Orient at 09.00 on 11 June.

They also captured approximately 1200 artillery pieces, 40000 muskets, 1,500,000 pounds (680,000 kg) of gunpowder, two ships of the line, a frigate and four galleys of the Order.

General Vaubois remained on the island with a garrison in order to maintain control, thereby establishing the French occupation of Malta.

During his short stay, Napoleon dictated instructions which radically reformed the Maltese government and society, so as to bring it in line with French Republican ideals.

[22] A few days after the capitulation, the Grand Master and many knights left the island, taking with them few movable possessions including some relics and icons.