From 1883 to 1898, the Sudan (then an Egyptian province) was closed by the insurrection of the Mahdi Mohammed Ahmed and his successor Abdallahi ibn Muhammad, and the missionaries were compelled to work outside the circuit of their jurisdiction in Egypt.

On 2 September 1898, the Anglo-Egyptian army, which in 1896 had begun operations for the recovery of the lost provinces, completed the overthrow of the Khalifa, although he was not slain until November of the following year.

The country suffered long from the effects of the 'Dervish' (Mahdist) oppression, during which it was largely depopulated, wide tracts having gone out of cultivation and trade having been abandoned.

The two religious congregations, the Sons of the Sacred Heart and the Pious Mothers of Nigritia, furnished missionaries and sisters to the vicariate, and the two periodical papers La Nigrizia (The Africaness, in Verona, Italy) and Stern der Neger ('Star of the Africans', in Brixen, then imperial Austria) print articles about this mission.

It lost territories again to establish missionary jurisdictions becoming current dioceses : On 12 December 1974, it was promoted as Metropolitan Archdiocese of Khartoum.