The Ohrid Archiepiscopate was the only medieval feudal institution that continued to exist in the time of the Turkish rule. Why the Turks decided to leave it active can only be assumed.

Whatever the reasons, the Archiepiscopate retained full internal autonomy and kept a large portion of its previous rights and privileges. This enabled it to fulfill its role. With the consent and support of the Turkish rulers, after a certain period of time, the Ohrid Archiepiscopate managed to expand its jurisdiction on new territories. In the first decades of XV century the jurisdiction of the Ohrid Archiepiscopate covered the eparchies of Sofia and Vidin. In the middle of XV century it had expanded to the eparchies of Vlaska and Moldavia, and prior to the re-establishment of the patriarchy of Pec, also the parts of the Serbian Church. In XVI century the Ohrid Archiepiscopate even managed to gain governance over the so-called Italian Eparchy, although only temporarily.

In order to survive, the feudal Ohrid Archiepiscopate gained benefits from certain taxes payable in goods and money, and free of charge labour. The free labour and taxes in kind were mainly practiced on special occasions, like holidays, religious feasts, whereas taxes payable in monies were collected in the form of fees. In addition, there was also the permanent annual tax. Thus, each Christian household paid 12 coins. The same tax was also paid by the clergy, but to the amount of one gold coin.

Folk stories transferred from generation to generation tell us that Ohrid had more than 300 churches – one church for each holiday in the year. However, after the arrival of the Turks the majority churches were ruined. According to one document, in XVII century there were 33 active churches, and in the beginning of XIX century only three town churches were in service.

There were times in the history of Ohrid Archiepiscopate when the entire territories were either seceded or alienated. The most dramatic example was that of Bishop Pavle of Smederevo who attempted to separate the Serbian eparchies from the Ohrid Archiepiscopate and re-establish the Pech Patriarchate. These efforts continued for rather a long period and lasted from 1527 to 1541. The Archbishop of Ohrid, Prohor, managed to convict these attempts three times before the Church Council. The Archbishops of Constantinople, Alexandria, Jerusalem, and Antioche followed suit.

During the rule of the Turks, the Archbishops from Ohrid used to travel to the Western European countries and to Russia to advocate for the liberation of the Balkans from the Turks. In that period certain bishops were inclined to the idea of a union with the Roman Church. The Ohrid Catholic Archbishopric was established in the middle XVII century, but in reality it never became active since the influence of Catholicism in Ohrid was futile.

In the second half of XVII century the Constantinople Patriarchate did not conceal its aspirations towards Ohrid Archiepiscopate. Due to certain disagreements between the Ohrid archpriests, the Patriarch of Constantinople promoted the Metropolitan Meletheus into Archbishop. His election led to the further internal conflicts within the Ohrid Archiepiscopate until its final abolishment. The conflicts were between the Fanariotes (pro-Greek inclined party), and the autochthonous party. In the fall of 1766, five metropolitans from the region of Ohrid signed the document with which they surrendered to the authority of the Constantinople Patriarch in Constantinople. Facing that situation, in January 1767 the Archbishop of Ohrid, Arsenius resigned from the Ohrid throne. Shortly after that, the Sultan passed a resolution for the abolishment of the Ohrid Archiepiscopate. All of its eparchies were annexed to the Constantinople Patriarchate. Also the Ohrid Eparchy, one of the 14 within the Ohrid Archiepiscopate as it was then, was abolished and adjoined to the Prespa Eparchy. Its full name was Prespa and Lychnidos Eparchy, indicating that Ohrid, once again, was renamed Lychnidos.

The XVIII century wars seriously shook the Ottoman Empire; thus the feudals were increasingly becoming more independent from the central Turkish rule. One who was significant for Ohrid was Gheladin Bey. He was pursued both by the central government and by some feudals. As a result Ohrid was devastated and the citizens were tortured. Human lives were highly endangered and people were dying in great numbers. In such circumstances, two plague epidemics – the first one in February 1810, and the second in the fall of 1816 struck Ohrid. Constant robberies occurred and therefore Gheladin Bey took in a soldier called Kuzman Kapidan to protect the people. A lot of folk songs have been written about this hero. He had a gang of about 40 brave and experienced men. In the period of Gheladin Bey the Empire wanted to strengthen its power, so the Sultan’s army attacked Ohrid. Almost the entire property of the Bey was confiscated, and in October 1832, Gheladin Bey flees as far as Egypt.