From 1788, the ambitious semi-independent Albanian ruler of Ioannina, Ali Pasha, coveted Karli-Eli and tried to gain control over it by intervening in its governance.

Albanian rulers Varaz Grigor and his son Djavanshir (616-681) were also from the dynasty of mehranids.

His first employment was as a folk physician to the court of Ali Pasha, the Albanian ruler of the Pashalik of Yanina, a position he held until 1803.

Since the early 14th century the power of the Despotate of Epirus had been decreasing while the Albanian rulers had been increasing their control over many areas of the despotate.

In the 13th and 14th century the city changed hands between the Despotate of Epirus, the Bulgarian, the Byzantine and the Serbian Empire and local Albanian rulers.

In 1385, the Albanian ruler of Durrës, Karl Thopia, appealed to the sultan for support against his rivals, the Balšić noble family.

The government under Skanderbeg was unstable, however, and at times local Albanian rulers cooperated with the Ottoman Turks against him.

In early 14th century, the city was under the rule of a coalition between Anjous, Hungarians and the Albanian rulers of the Thopia family.

After suffering heavy losses, the Byzantines were finally able to control the situation, but in the years 1260-1270 the Albanian rulers revolted again in the region of Dyrrhachium.

The Despotate of Arta was a despotate established by Albanian rulers during the 14th century, when Albanian tribes moved into Epirus and founded two short-lived principalities there.