A wealthy Order of Knights drawn exclusively from the ranks of the nobility was sure to attract the attention of the French revolutionaries. Its international character was a cause of offence to the strong French nationalism engendered during the Revolution, while its traces of monastic organisation helped to identify the Knights with the Church.

When Necker, in the financial distress of the autumn of 1789, appealed for a voluntary contribution from all landowners, the Order gave him a third of the revenue of its French commanderies, and later it pledged its credit for 500,000 francs to the destitute Louis XVI., to help him in the flight that ended so disastrously at Varennes. This last act put it in definite opposition to the Revolution.

The Constituent Assembly declared the Order of St. John to be a foreign Power possessing property in France, and, as such, liable to all taxes to be levied on natives, and immediately afterwards a decree was passed declaring that any Frenchman belonging to an Order of Knighthood which demanded proofs of nobility from entrants could not be considered a French citizen. This was followed by the main attack on September 19, 1792, when all the property in France was declared confiscate and annexed to the French national domains. There was some mention of indemnification to the despoiled Knights, but as the necessary condition to a pension was residence in France - a dangerous course for a noble in 1793 and 1794 - the scheme came to naught. The decree of September, 1792, was the death-blow to the Order, and its extinction was simply a matter of time. The course of the war and the constant French successes made their position even more perilous. Half the revenues had gone with the confiscation in France; but this was not all, for Bonaparte's Italian campaigns meant the loss of the Order's estates in Northern Italy, and the conquests of the French on the Rhine diminished the German possessions. With decreasing resources and dwindling numbers, the fortress of Malta could not long hold out if attacked, and the position of the Order was becoming desperate. De Rohan, the Grand Master, temporised and refused to declare war on France, but he seems to have helped the Spanish and English fleets by allowing them to recruit at Malta, a privilege hitherto granted very sparingly by the Knights. But whatever the Grand Master's policy, no words or pretences could disguise the fact that the French Republic by its confiscation had assaulted the Order. It was only too probable that France would seize the first opportunity of attacking the Order in its own home and by this means increasing its power in the Mediterranean.

One gleam of light came to cheer the gloom at Malta. The third dismemberment of Poland had brought the Polish Priory into the hands of the Tsar Paul I. Among other eccentricities of that monarch was a passionate admiration for chivalry, which he displayed by changing the Polish into a Russian Priory, increasing its revenues to 300,000 florins, and incorporating it in the Anglo-Bavarian langue; he also assumed the title of "Protector of the Order of Malta."

In 1797, at Ancona, Napoleon had intercepted a message from the Tsar to the Grand Master containing this news. Plans for the capture of Malta took shape in Bonaparte's mind, and he sent a cousin of the French consul at Malta, Poussielgue by name, to spy out the condition of the island, at the same time ordering Admiral Brueys, on his journey from Corfu to Toulon, to examine the situation of Malta. When the expedition to Egypt was decided upon, the capture of Malta formed part of the instructions to Napoleon.

Bonaparte, relying on the demoralisation of the island, intended the capture to be a swift piece of work, and Poussielgue had helped him by winning over some natives and French Knights to his side. The Grand Master, Von Hompesch, seems to have been utterly unnerved by the bewildering problems before him, and the cowardice and irresolution he displayed were a disgrace to the traditions of the Order. Speed was essential to the French army, as discovery by Nelson would be fatal to Bonaparte's plans, but had Von Hompesch been an utter traitor the capitulation could not have been more sudden and disgraceful and beneficial to the enemy.

On June 6 the vanguard of the French appeared off the island, and on the 9th it was joined by the main fleet, the whole now numbering about 450 sail, of which 14 were ships of the line and 30 were frigates; the Grand Master had about 300 Knights and 6,000 men, chiefly Maltese, under arms. Had this garrison been resolute and united, the fortifications of Valetta could have held the French for a considerable time. But the natives were divided, many regarding the French, despite their doubtful career of the last few years, as liberators from a detestable tyranny. Two-thirds of the Knights were French, and many of them had become infected with republican principles, though the French langues also contained the fiercest opponents to the invaders.