After seven years of moving from place to place in Europe the Knights became established in 1530 when the Holy Roman Emperor, King Charles V of Spain, as King of Sicily, gave them Malta, Gozo and the North African port of Tripoli in perpetual fiefdom in exchange for an annual fee of a single Maltese falcon, which they were to send on All Souls Day to the King's representative, the Viceroy of Sicily. (This historical fact was used as the plot hook in Dashiell Hammett's famous book The Maltese Falcon.)
The Hospitallers continued their actions against the Muslims and especially the Barbary pirates. Although they had only few ships they quickly drew the ire of the Ottomans, who were unhappy to see the order resettled. In 1565 Suleiman sent an invasion force of about 40,000 men to besiege the 700 knights and 8000 soldiers and expel them from Malta.
At first the battle went as badly for the Hospitallers as Rhodes had: most of the cities were destroyed and about half the knights killed. On 18 August the position of the besieged was becoming desperate: dwindling daily in numbers, they were becoming too feeble to hold the long line of fortifications. But when his council suggested the abandonment of Il Borgo and Senglea and withdrawal to Fort St. Angelo, Grand Master Jean Parisot de la Valette refused.
The Viceroy of Sicily had not sent help; possibly the Viceroy's orders from Philip II of Spain were so obscurely worded as to put on his own shoulders the burden of the decision whether to help the Knights at the expense of his own defenses. A wrong decision could mean defeat and exposing Sicily and Naples to the Ottomans. He had left his own son with La Valette, so he could hardly be indifferent to the fate of the fortress. Whatever may have been the cause of his delay, the Viceroy hesitated until the battle had almost been decided by the unaided efforts of the Knights, before being forced to move by the indignation of his own officers.
On 23 August came yet another grand assault, the last serious effort, as it proved, of the besiegers. It was thrown back with the greatest difficulty, even the wounded taking part in the defense. The plight of the Turkish forces, however, was now desperate. With the exception of Fort St. Elmo, the fortifications were still intact. Working night and day the garrison had repaired the breaches, and the capture of Malta seemed more and more impossible. Many of the Ottoman troops in crowded quarters had fallen ill over the terrible summer months. Ammunition and food were beginning to run short, and the Ottoman troops were becoming increasingly dispirited at the failure of their attacks and their losses. The death on 23 June of skilled commander Dragut, a corsair and admiral of the Ottoman fleet, was a serious blow. The Turkish commanders, Piyale Pasha and Mustafa Pasha, were careless. They had a huge fleet which they used with effect on only one occasion. They neglected their communications with the African coast and made no attempt to watch and intercept Sicilian reinforcements.
On 1 September they made their last effort, but the morale of the Ottoman troops had deteriorated seriously and the attack was feeble, to the great encouragement of the besieged, who now began to see hopes of deliverance. The perplexed and indecisive Ottomans heard of the arrival of Sicilian reinforcements in Mellieħa Bay. Unaware that the force was very small, they broke off the siege and left on 8 September. The Great Siege of Malta may have been the last action in which a force of knights won a decisive victory.
When the Ottomans departed the Hospitallers had 600 men able to bear arms. The most reliable estimate puts the number of the Ottoman army at its height at some 40,000 men, of whom 15,000 eventually returned to Constantinople. The siege is portrayed vividly in the frescoes of Matteo Perez d'Aleccio in the Hall of St. Michael and St. George, also known as the Throne Room, in the Grand Master's Palace in Valletta. Four of the original modellos, painted in oils by Perez d'Aleccio between 1576 and 1581, can be found in the Cube Room of the Queen's House at Greenwich, London. After the siege a new city had to be built – the present city named Valletta in memory of the Grand Master who had withstood the siege.
In 1607 the Grand Master of the Hospitallers was granted the status of Reichsfürst (Prince of the Holy Roman Empire, even though the Order's territory was always south of the Holy Roman Empire). In 1630 the Grand Master was awarded ecclesiastic equality with cardinals, and the unique hybrid style His Most Eminent Highness, reflecting both qualities qualifying him as a true Prince of the Church.
Following the Christian victory over the Ottoman fleet in the Battle of Lepanto in 1571, the Knights continued to attack pirates and Muslim shipping, and their base became a centre for slave trading well into the 18th century, selling captured Africans and Turks and freeing Christian slaves. A thousand slaves were needed to equip and man each of the Order's galleys
The Order lost many of its European holdings following the rise of Protestantism, but survived on Malta. The property of the English branch was confiscated in 1540. In 1577, the German Bailiwick of Brandenburg became Lutheran, but continued to pay its financial contribution to the Order until the branch was turned into a merit Order by the King of Prussia in 1812. The "Johanniter Orden" was restored as a Prussian Order of Knights Hospitaller in 1852.
Baron Vassiliev, a 19th-century Knight Commander. The Knights of Malta had a strong presence within the Imperial Russian Navy and the pre-revolutionary French Navy. When De Poincy was appointed governor of the French colony on St. Kitts in 1639 he was a prominent Knight of St. John and dressed his retinue with the emblems of the order. The Order's presence in the Caribbean was eclipsed with his death in 1660. He also bought the island of Saint Croix as his personal estate and deeded it to the Knights of St. John. In 1665, St. Croix was bought by the French West India Company, ending the Order's presence in the Caribbean.
In 1789 France erupted in revolution and anti-clerical and anti-aristocratic furor, forcing many French knights and nobles to flee for their lives. Many of the Order's traditional sources of revenue from France were lost permanently.
The decree of the French National Assembly Abolishing the Feudal System (1789) abolished the Order in France: V. Tithes of every description, as well as the dues which have been substituted for them, under whatever denomination they are known or collected (even when compounded for), possessed by secular or regular congregations, by holders of benefices, members of corporations (including the Order of Malta and other religious and military orders), as well as those devoted to the maintenance of churches, those impropriated to lay persons and those substituted for the portion congrue, are abolished (...) (The Decree Abolishing the Feudal System, August 11, 1789, J.H. Robinson, ed., Readings in European History 2 vols. (Boston: Ginn, 1906), 2: 404-409) The French Revolutionary Government seized the assets and properties of the Order in France in 1792.
Their Mediterranean stronghold of Malta was captured by Napoleon in 1798 during his expedition to Egypt. As a ruse, Napoleon asked for safe harbor to resupply his ships, and then turned against his hosts once safely inside Valletta. Grand Master Ferdinand von Hompesch zu Bolheim failed to anticipate or prepare for this threat, provided no effective leadership, and readily capitulated to Napoleon, arguing that the order's charter prohibited fighting against Christians. He resigned his office and retreated into obscurity. The order continued to exist in a diminished form and negotiated with European governments for a return to power. The Tsar of Russia gave the largest number of knights shelter in St. Petersburg and this gave rise to the Russian tradition of the Knights Hospitaller and recognition within the Russian Imperial Orders.
In 1798, following Napoleon's taking of Malta, the order was dispersed, but with a large number of refugee knights sheltering in St Petersburg, where they elected the Russian Emperor, Paul I as their Grand Master – a rival to Grand Master Ferdinand Hompesch, then held in disgrace. Hompesch abdicated in 1799, under pressure from the Austrian Court, leaving Paul as the de facto Grand Master. As Grand Master Paul I created, in addition to the Roman Catholic Grand Priory, a Russian tradition within the Hospitaller Order – the "Russian Grand Priory" of no less than 118 Commanderies dwarfing the rest of the Order, and open to all Christians. Paul's election as Grand Master was never ratified under Roman Catholic Canon law, and the Russian Priory was a de facto rather than a de jure part of the Roman Catholic Order.
By the early 1800s, the order had been severely weakened by the loss of its priories throughout Europe. Only 10% of the order's income came from traditional sources in Europe, with the remaining 90% being generated by the Russian Grand Priory until 1810. This was partly reflected in the government of the Order being under Lieutenants, rather than Grand Masters in the period 1805 to 1879, when Pope Leo XIII restored a Grand Master to the order. This signaled the renewal of the order's fortunes as a humanitarian and religious organization. Hospitaller work, the original work of the order, became once again its main concern. The hospital and welfare activities, undertaken on a considerable scale in World War I, were greatly intensified and expanded in World War II under the Grand Master Fra' Ludovico Chigi della Rovere Albani (Grand Master 1931-1951).
In 1834, the revived Order established a new headquarters in Rome. The Sovereign Military Hospitaller Order of Saint John of Jerusalem, of Rhodes and of Malta, better known as the Sovereign Military Order of Malta (SMOM), remains a Roman Catholic religious order which claims sovereignty under international law and has been granted permanent observer status at the United Nations, although its claims of sovereignty are disputed by a handful of scholars.