Relations between the Fatimids and Nubia were renewed as a result of the increased influence of the viziers during the reign of Caliph Al-Adid. If the Nubian kings seized the opportunity of Egypt's weakness and raided it, as long as its caliphs no longer had more than the shadow of authority, the Nubian king gathered an army of ten thousand horsemen and attacked the city of Aswan, where he killed many Muslims. This was in the year 556 AH / 1161 AD. The sources do not mention the military measures taken by the Fatimids in response to this treacherous Nubian attack and their stance on it.

Nubia, in the late Fatimid era, became a refuge and sanctuary for senior Fatimid state officials fleeing the dangers that threatened them.

During the period of good Fatimid relations with Nubia, the Fatimids controlled eastern trade, and the port of (Suez) was the port from which grain was sent to the Hijaz. However, they found that it was not suitable as a port for that purpose, as they found what they were looking for in the port of (Aydhab), as it was closer to the Hijaz and also closer to Yemen than Bilazm. In addition to the presence of a strong ruler in the city of (Qus) who facilitated the movement and transit to the port of (Aydhab), thus shortening the sea journey, which was fraught with danger. Moreover, the port of Aydhab was not far from the port of Jeddah.

The movement of pilgrims to the Aydhab route during the reign of Caliph Al-Mustansir Billah Al-Fatimi (477-487 AH / 1084-1094 AD), whose reign was long, was a good opportunity for the spread of Islam to the south, as some pilgrims preferred to stay in Aydhab upon their return and then head south to the land of Baham or Nubia. The Aydhab route became the main pilgrimage route for a period exceeding two centuries, which ended in the year (461 AH / 1268 AD). At the end of the twelfth century AD, Aydhab became one of the most important ports in the Islamic world and was a meeting point for merchant ships from India, Yemen, East Africa, and Jeddah, from where caravans departed under the supervision of Arab tribes, including 71.