The Kushite kingdom collapsed during the 4th century AD due to a decline in trade and persistent raiding by desert nomads. By the 6th century AD three kingdoms existed in the southern Nile valley – Makuria (an area which largely corresponded with Upper Nubia), Nobatia (in Lower Nubia) and Alwa in the south. Nobatia was incorporated into Makuria in the mid-7th century.

During the 6th century, the Nubian kingdoms were converted to Christianity by Byzantine missionaries. Churches, monasteries and cathedrals were constructed, with interiors decorated with paintings. The churches built in Nubia were similar to the early Christian basilicas that had been constructed in the Byzantine Empire. The cathedral built at Faras is renowned for its series of Christian murals depicting saints, bishops, kings and archangels. Byzantine, Coptic, Syro-Palestinian and local influences are all identifiable in these murals.

The highest ranking bishops had their seats at Faras and Old Dongola in Makuria. Egypt and Nubia maintained close ties during this period as the Egyptian and Nubian churches were affiliated and some Nubian bishops were consecrated at Alexandria in Egypt.