Greeks in Malta (; ) have a long presence in Malta, which may lead back to ancient history. The archipelago was intensely Hellenized beginning in the 3rd century BC, a process which intertwined with the Christianization of Malta after the 1st century AD. The Byzantine presence was overturned by the Arab conquest of 870, and the surviving Greek community was Islamified. Maltese Christianity of the Byzantine Rite was only preserved in some parts of the country, being especially important in Gozo. These groups formed the basis for a local branch of the Eastern Orthodox Church, revived following Norman conquest in the 1120s. Although marginalized by Catholicism, which became the dominant faith, a Greek-speaking Eastern Orthodox community survived into the 15th century.

Greek immigration was resumed in the 1520s, shortly before the establishment of Hospitaller Malta. It comprised mainly refugees from the Ottoman Empire, hundreds or thousands of whom escaped from Rhodes. They reestablished the Greek Orthodox colony, presumed to have been placed under the Archbishopric of Ohrid, but also included in their ranks Greek-speaking members of both the Latin Church and Greek Byzantine Catholic Church. Within fifty years, with the onset of Counter-Reformation, the former community was pressured into merging with the latter two. By 1600, the Eastern Orthodox Greeks had formally abjured, but in various documented cases continued to practice their older rites. In tandem, the consolidated community of Catholic Greeks discarded its traditional center in Birgu and moved its base to Valletta, after which it became prone to assimilation into the ethnic mainstream.

In the 17th century, the Eastern Orthodox presence was also reinforced by Ottoman Greeks taken as slaves by the Maltese privateers, some of whom were themselves ethnic Greeks; there were also new waves of Maniots and Aetolians. Though small in numbers, the resulting community participated in the propagation of Greek nationalism and of the "Greek Plan". Many local Greeks also supported the French occupation of Malta, which closely preceded a Franco–Ottoman war. During the period of British colonization, the Maltese Greek community leader Ioannis Papafis was a sponsor of the Greek War of Independence. Greeks affiliated with either Catholicism or Eastern Orthodoxy remained present over the following centuries, though the latter community continued to be informally marginalized throughout the 19th century, and are now a small minority.

Early presence Various archeological finds may suggest some connections between the old Maltese civilization and the Minoan civilization, followed by Mycenaean Greece. In the 1920s, biological anthropologist L. H. Dudley Buxton proposed that the original inhabitants of Malta Island and Gozo were Cretan immigrants. However, the Ancient Greeks appear not to have included either island in their colonization of the Mediterranean, perhaps owing to their lack of natural resources. They used Malta for commerce, but the archipelago was taken over and colonized by Phoenicians, then by Carthage. Gozo is perhaps the mythical island of Ogygia, described in the Odyssey, which may attest that groups of Mycenaeans once settled there. The main island was known in Greece under the name Melite (); one theory is that the name "Malta" is a derivative of the Greek word for "honey" (). A Phoenician derivation has also been proposed.

Despite being under Carthaginian rule, Malta was culturally integrated by the Hellenistic world in the 3rd century BC, when it built strong commercial links with Magna Graecia. Focusing on the finds at Tas-Silġ, scholar Antonio Tempio proposes that the archipelago was regularly visited by traders from Pithekoūsai, which had a mixed Carthaginian–Greek populace. Greek influence was only reinforced after the First Punic War, when Malta was annexed to the Roman Republic, later becoming part of the Roman Empire alongside Roman Greece. This was especially the case in Gozo, where archeological finds document the extensive circulation of Ancient Greek coinage. While Punic was still spoken locally into the 1st century AD and perhaps even later, it faced competition from both Latin and Greek (see Cippi of Melqart).

The Greek-speaking Byzantine Empire held Malta from the 6th century AD, and, beginning in the 8th century, Maltese Christianity was organized under the Byzantine Rite. Scant archeological evidence may suggest that local communities were under the command of tourmarchoi representing the Sicilian Theme, but this remains disputed. In circa 870, following the islands' capture and annexation by the Emirate of Sicily, some 3,000 men were reportedly killed, while 3,600 women and 5,000 children fell victim the Arab slave trade. The remaining Greek community was persecuted, its bishop enslaved, and its church destroyed. Local Greeks were largely converted to Islam, but continued to speak their original language.

The period of Islamic conversion also witnessed the birth of Maltese, which developed largely from Maghrebi and Siculo-Arabic. Medieval Greek left "remarkably few" or "absolutely no traces" on this linguistic development. There is however evidence that a Christian church, probably Byzantine, still survived on Gozo, though it was cut off from contacts with other parts of Europe. An historical account originating with Zakariya al-Qazwini suggests that in the 11th century the Catepanate of Italy tried to restore Christian Byzantine rule over Malta. This attempt was thwarted when the Arabs agreed to emancipate their slaves, who joined the resistance. Nevertheless, the ethnic origin of these men remains unclear.

Norman-Byzantine and Rhodian diasporas

Following the Norman conquest of the 1120s, Malta was integrated with the County, then the Kingdom of Sicily, and as such included within the Norman–Byzantine cultural sphere. The new rulers released and sent back to their homes those Christian slaves still present on the islands, but also brought with them a number of Greeks, who were disproportionately represented in the Norman–Sicilian navy. During the brief existence of a Norman kingdom in Africa, Greek administrators participated in repressing Arab piracy. A poem by a Greek exile to Malta, probably authored ca. 1150, laments that the population was still mostly Muslim, and commends the Normans for their efforts to convert them.

Upon the end of that campaign, which can be reliably dated to the 13th century, Maltese Arabs and Greek Muslims were generally converted to Catholicism. There is however evidence that at least some Maltese Greeks opted for the Eastern Orthodox Church (see East–West Schism). Some clandestine sanctuaries might be indicators that Basilian monks, perhaps affiliated with Eastern Orthodoxy, were active in Malta. An obituary discovered in 2012 mentions a Nicólaos Protopapàs Máltes (died 1230). His Greek surname, which can be read as "Protopope", could suggest that Eastern Orthodoxy had maintained an ecclesiastical structure. In the 1260s, Sicily and Malta became part of a personal empire built by Charles I of Anjou. According to anthropologist Stefan Goodwin, at his stage "faltering religious pluralism still existed in the sense that Orthodox Christians, Jews, and Muslims still constituted a substantial minority of the population." Malta's native Greek Orthodoxy probably died out in the mid 15th century.

Other groups of Greeks appeared in that context. In July 1401, the Crown of Aragon (which included Sicily and Malta from 1409) banned the release of Greek, Circassian, Albanian, Ruthenian, Bulgarian and Vlach slaves. From the 16th century on, most Greeks who arrived in Malta did so as a result of displacement by the Ottoman Empire (see Ottoman wars in Europe). Following a siege in 1522, the Knights Hospitaller were chased out Rhodes and granted possession of Malta. Rhodian Greeks followed them there, numbering in the hundreds or as many as 3,000 to 5,000 individuals (up to 20% of the total population). Overall, most migrants were initially Eastern Orthodox—however, Rhodians most likely included parishoners of the Latin Church and Greek Byzantine Catholics.

Eastern Orthodox and Catholic Greeks from Hospitaller Malta and Maltese-occupied Tripoli were granted the privilege of trading with Muslim states, and integrated commercially with the larger Greek diaspora. In tandem, Greek seafarers contributed to the birth of Maltese privateering. Already in the 1530s, the archipelago was home to prosperous Greek Maltese merchants Sydero Metaxí and Stammato Galanti. Eastern Orthodox Rhodians settled in Malta-proper included priest Angelo Metaxí and the prosperous Fundomali family of Birgu. Among the Catholic descendants of this Rhodian diaspora was the adventurer Iacob Heraclid. Born at Birkirkara in 1527, he claimed the thrones of Samos and Chios, and would eventually serve as Prince of Moldavia in the 1560s. Propagated and partly distorted by the Hospitallers, accounts of Heraclid's career have left traces in Maltese literature and historiography.

With four parish churches mentioned in early records, Birgu remained the center of Greek Rhodian immigration. In 1565, during the Great Siege of Malta, Greeks from that town joined a militia company mainly staffed by Maltese locals. Following the Hospitaller relocation from Birgu to Valletta, Greek converts were invited to the latter city, and were granted the Church of St Nicholas. Despite being a Catholic state, Hospitaller Malta remained somewhat tolerant of the Orthodox presence and, by 1621, the Greek Orthodox community in the archipelago had established direct contacts with the Patriarchate of Constantinople. It is likely that Malta and Gozo answered to the Archbishopric of Ohrid, through a suffragan located at Agrigento.

Inquisition and assimilation During the Counter-Reformation era, efforts to absorb this congregation into Catholicism became more systematic. Greeks who were still Eastern Orthodox made repeated pledges of union with Catholicism, as a Byzantine Rite Eastern Catholic community, but these remained formal. In the 1570s, Cardinal Giulio Antonio Santoro and the Roman Inquisition made a note that the Greek "heretics" were resisting such attempts, taking their chrism exclusively from their "Oriental prelate". In 1575 Birgu, there were 74 Greek Catholics. Their parish priest, Emmanuel Metaxí, angered Catholic supervisors by omitting references to Filioque and ignoring the Gregorian calendar. Other Byzantine-Rite Greeks were prosecuted for similar offenses involving the calendar, prompting priest Constantin Sguro to ask advice from the Holy See. In one other case, the five daughters of a Greek priest were formally investigated by the Inquisition after accusations that they practiced witchcraft using his leftover chrism. In 1600, Metaxí bequeathed Damascena Church to monks from the Church of Sinai; unusually, this transfer was countersigned by the Catholic Archbishop, Tomás Gargallo. The monks, who also catered to the needs of Greeks in Cospicua, were presumed to be Catholic converts, but later found to be omitting the Filioque.