Coptic patriarch of Alexandria rather than under the patriarch of Constantinople. However, the Nubians always used Greek rather than Coptic as their liturgical language.

Protected by the Baqt treaty, the medieval Nubians enjoyed once again a prosperous trade with Egypt throughout the Middle Ages. Relations were especially close with the Egyptian Fatimid Caliphate (969–1171), which was often on bad terms with other Islamic powers and depended heavily on the support of Nubian troops. In these circumstances of prolonged peace and prosperity, Nubian civilization flourished once again as it had in Kushite times, and there were major developments in architecture and art as well as in several crafts. As in earlier times, the most outstanding achievements were in the religious sphere, but iconography now always emphasized a heavenly rather than an earthly king. No royal monuments of any kind have been found from the entire medieval period, and the names of only a few of the kings are known, mainly from Arabic records. Nevertheless, the indigenous language (now usually called Old Nubian) was once again written, this time in a modified Greek alphabet. It was used mainly for administrative and commercial correspondence while religious documents were usually in Greek. There was also widespread literacy in Arabic as a result of the extensive trade with Egypt.

When the warlike Mamluks seized control in Egypt in 1250, they repudiated the Baqt treaty and began an intermittent series of military incursions into Nubia. At the same time, the monarchy at Dongola was weakened by dynastic quarrels, and local magnates began increasingly to assert their authority. The final blow to Nubia’s medieval civilization came from the massive Arab nomad migrations, some from Egypt and some directly from the Arabian peninsula, that overran the central Sudan in the fourteenth to sixteenth centuries. Many of the newcomers settled along the Nile and intermarried with the Nubian population; at the same time, they destroyed the older kingdoms and divided their territory up into a series of petty warring principalities after the fashion of Arab tribes.

Lower Nubia was largely spared from these ravages because of its total lack of pastoral resources, and a splinter Christian kingdom called Dotawo survived there until near the end of the fifteenth century. However, contact with the church in Egypt had been lost by this time, and Nubian Christianity gradually died out because of a lack of a trained priesthood. When the Ottoman Turks, who had conquered Egypt in 1517, added Lower Nubia to their dominions half a century later, they found no surviving trace either of the Dotawo kingdom or of an established church.

The centuries that followed were a time of political anarchy and economic and cultural impoverishment. Ottoman rule in the north was wholly extractive and corrupt while further to the south, warlike tribes and principalities formed a series of endlessly shifting coalitions. Meanwhile, the development of European maritime trade with the African coasts had almost wholly supplanted the Nile trade route. The written Nubian language and all the great architectural and artistic achievements of the medieval period were lost, and the mass of Nubians reverted to a purely subsistence economy and a condition of life hardly different from that of the Neolithic period. Many people clung to remnants of their older Christian faith, but there was no established religion until, in the seventeenth century, Islamic teachers from North and West Africa came as missionaries and established religious schools, mainly in the area around present-day Khartoum. In the prevailing cultural and ideological vacuum of the times, the new religion spread rapidly, laying the foundations for the basically Islamic civilization of northern Sudan today.

The Arab migrations set in motion a process of linguistic displacement as the indigenous Nubian languages gave way to Arabic. The process began in central Sudan, and from there has been spreading gradually northward down to the present day. As a result, the Nubian languages now survive only in Egyptian Nubia and the most northerly part of the Sudan. Today, the term Nubia is applied, in an ethnic and linguistic sense, only to the region where Nubian is still spoken, although archaeologists and culture historians continue to employ it in its older and broader sense.