The peace treaty was concluded in March 1573 with Venice agreeing both to pay a heavy war indemnity sufficient to cover all the Sultan's expenses incurred in the conflict, and to renounce all Venetian claims on Cyprus. The local population  somehow collaborated with the invaders, as the first step of the Ottoman governors was to abolish the feudal system, giving ownership of the land to the peasant families who had worked there.

The Orthodox Church was freed from centuries of control by the Latin hierarchy and its previous tradition of independence reaffirmed under the restored archbishopric. On the other hand, the Catholic Crusader church and the Venetian rulers were expelled. Their buildings were confiscated and converted into mosques or sold to the Orthodox Church. Catholicism became a punishable offense, so Catholics were forced to choose between converting to Orthodox Christianity, converting to Islam or exile. The majority chose Orthodox Christianity, but the result was that the population began to assume the ethnic structure that it still possesses today, that is, the division between the Greek population and the Turkish population.

After the defeat of the Venetians, Lala Mustafa Pasha, the Turkish commander, chose 12,000 soldiers to remain on the island for the formation of the defensive garrison of Famagusta, Nicosia and Kyrenia. The military forces were integrated by another 20,000 unarmed soldiers and 2,000 knights left as colonists. These people formed the original nucleus of the nascent Turkish Cypriot community whose members were of Turkish origin. Measures were also taken to assist all soldiers with ties on the mainland to bring their wives and children to Cyprus.

However, in the opinion of Sinan Pasha, who replaced Lala Mustafa Pasha, the island was still heavily in need not only of more residents in general, but also of skilled craftsmen. Consequently, Sultan Selim II issued a decree for the transfer of one in ten families from the area of ​​(modern) Southern Turkey.

In addition, they had families with many young daughters transferred to provide spouses to former unmarried soldiers. A total of 5,720 families were relocated in this initial period to around one hundred empty villages in Cyprus.

The use of resettlement as a general method for the development of the Turkish population of Cyprus continued intermittently until the mid-eighteenth century. At the time of the British arrival in Cyprus in 1878 under the Cyprus Defense Alliance between Great Britain and the Ottoman Empire, about 95,000 Turkish Cypriots resided on the island.

The Ottoman conquest of Cyprus coincided with the gradual stagnation of the economy of the Near East due to the discovery of the Atlantic trade routes in the mid-fifteenth century. Within a century, the crowded waters of the Eastern Mediterranean had become an abandoned stagnation. Many of the profitable crops, such as sugar, were ruined by American competition in the 17th century. This was partially compensated by the cotton plantations which allowed to create a tradition of production of fine fabrics. Morphou exported linen, the Marathasa valley was known for its woollen clothing and Nicosia famous for its silks and gold embroidery.

During this period there was a series of taxed armed revolts that often united both the Greek and Turkish against a particularly stingy governor or community leader ruler. The governor's (pasha) office sales system, an ethnic group's collection of taxes and agriculture, or the auctioning of taxes, helped create a powerful group of community leaders on the island.

The then governor of the island, although he had commanded a small garrison of 3,000 soldiers, was relatively helpless. He exercised authority for a short time and was mainly interested in recovering the purchase of his office with minimal effort and maximum profit, which he managed only through the leaders of the Turkish community and the Greek bishops.

The archbishop became particularly influential and in 1660 he was recognized as an official representative of the Greek Cypriots, with direct access rights to the Sultan's palace in Istanbul. In 1754 the archbishop was appointed responsible for the collection of taxes and later obtained the right to appoint the head of the civil service. By the early 19th century, the archbishop had become almost more important than the governor.

In 1814, the Greek nationalists on the mainland formed a secret organization called Friendly Company (Filiki Eteria). With the support of the rich communities of Greek exiles in Britain and the United States, the help of sympathizers in Western Europe and secret assistance from Russia, they planned a rebellion to gain independence from the Ottomans. The start of the uprising can be set for March 6, 1821 when several Greek officers of the Russian army crossed the Prut River in Romania. Concurrent outbreaks were planned across Greece, including Macedonia, Crete and Cyprus.

It turned out that the archbishop of Cyprus, along with other clergy members and major Christians, had ties to Filika Eteria. The governor's response was swift and bloody. The archbishop, bishops and many eminent Christians were massacred, resulting in the purging of Christians from the island. Some fled the country or fled to the European consuls in Larnaca.

Meanwhile the vast Ottoman Empire was showing signs of disintegration. After crushing the Greek uprising with the help of Egyptian governor Mohammed Ali, European powers intervened, resulting in the creation of an independent Greek kingdom in 1832. At the same time, Mohammed Ali inflicted defeat on his Ottoman masters and established an independent dynasty in Egypt.

The war with Russia, which had continued since 1769, when the Russians gained access through the Bosporus, weakened the Ottoman Empire and, after further defeats in 1877, some territory of Anatolia was ceded to the Russians. This alarmed the British, who saw the Russian advance as a threat to the Suez Canal which had been opened in 1869. An agreement was subsequently reached in 1878 that England would occupy Cyprus, using it as a base to protect its interests. and defend Ottoman territory against further invasions by Russia.