The Shona people of the Mwene Mutapa Empire worshipped a supreme god called Mwari, the creator of the world and everything in it. A central role in Shona-Karanga religion was played the mhondoro, the spirits of the ancestors of the ruling families. It was through these spirits that the Shona could talk to Mwari. Remembering the names of all the spirits and the task of calling on them in times of need was the responsibility of the nobles. Thus, the king of Mwene Mutapa played the role of high priest as well as acting as day-to-day ruler.

The Kongo kingdom in south-central Africa accepted Christianity in 1490 under King Nzinga Nkuwu. After King Nzinga Mpangu, Kongo power declined as Portuguese influence increased. King Alphonso I died in 1541, and his son Henrique, the first African bishop, attempted to establish a distinct African Christian church in the Kongo but failed. Most of the region later became the Portuguese colony of Angola.

While the fertile farm lands of parts of west, central and east Africa could support dense populations, the soil in southern Africa could not support large populations. However, relatively strong and centralized Bantu states did arise, the first among these were the Swazi, Ngoni and Xhosa peoples.

In 1652, the Dutch East India Company founded Cape Town as a port and supply base on the long voyage from Europe to the East Indies.