The native land of the Seljuks, established by Seljuk Bey from Oguz Turks, was central Asia. The Seljuks, who converted to Islam spreading towards north in the 10th century, tried to extend their power fighting against the tribes which had not been converted. The defeat and the capture of teh Byzantine Emperor Romanos Diogenes in 1071 by Alparslan, the great grandson of Seljuk By resulted in the decline of the Byzantine Empire and the beginning of a new era in the history of Anatolia.

In 1075 the Anatolian Seljuk State was founded. In 1082 Kayseri was conquered by Turks and Cappadocia came under Seljuk rule. Anatolia, which was an important region where Christianity had spread, became part of Islamic world which covered a large area; from North Africa, to Middle Asia and to the Near East. The conquest of Anatolia by Seljuk Turks did not influence the administrative authority of the patriarchy. We know this because in inscriptions from the 13th century found in the church of St George in the Ihlara region, names of the Seljuk Sultan Mesud II and the Byzantine Emperor Andronicus are treated with admiration. As a result of the decline of the Anatolian Seljuk State at the end of the 13th century, small beyliks (domains of minor rulers) came into being in different parts of Anatolia. In 1308, the IIkhanids, of Mongolian origin, invaded Anatolia and destroyed Kayseri, one of the important cities in the Cappadocia Region. Seljuk Sultans were controlled by the Mongolians and could not act independently. From then on, Anatolia was administered by the beyliks founded by different Turkish tribes.