In Africa, the Moravian Church in South Africa (MCSA) and the Presbyterian Church of Ghana (PCG) belong to the EMS Fellowship. Through the Basel Mission German Branch, the EMS is also linked to Cameroon, South Sudan and Nigeria and through the Mission Association of the Moravian Church in Germany to Tanzania.

Since its members are on the whole very poor, the African parishes often have to struggle with financial difficulties. The churches are particularly committed to health, rural development, peace work and the fight against HIV and AIDS. In addition, there are projects to improve school education, theological training and work with handicapped people.