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John of Ephesus' account describes the events around the Christianization of Alodia in detail. As the southernmost of the three Nubian kingdoms, Alodia was the last to be converted to Christianity. According to John, the Alodian King was aware of the conversion of Nobadia in 543 and asked him to send a bishop who would also baptize his people. The request was granted in 580, leading to the baptism of the King, his family and the local nobility. Thus, Alodia became a part of the Christian world under the Coptic Patriarchate of Alexandria. After conversion, several pagan temples, such as the one in Musawwarat es-Sufra, were probably converted into churches. The extent and speed with which Christianity spread among the Alodian populace is uncertain. Despite the conversion of the nobility, it is likely that Christianization of the rural population would have proceeded slowly, if at all.Between 639 and 641, Muslim Arabs conquered Egypt from the Byzantine Empire. Makuria, which by this time had been unified with Nobadia, fended off two subsequent Muslim invasions, one in 641/642 and another in 652. In the aftermath, Makuria and the Arabs agreed to sign the Baqt, a peace treaty that included a yearly exchange of gifts and socioeconomic regulations between Arabs and Nubians. Alodia was explicitly mentioned in the treaty as not being affected by it. While the Arabs failed to conquer Nubia, they began to settle along the western coast of the Red Sea. They founded the port towns of Aydhab and Badi in the 7th century and Suakin, first mentioned in the 10th century. From the 9th century, they pushed further inland, settling among the Beja throughout the Eastern Desert. Arab influence would remain confined to the east of the Nile until the 14th century.

Nobadia