Well that’s a huge question. One of the reasons is that most of Africa wasn’t conquered by either the Romans or the Mongols. If you weren’t in a position to obtain the technology behind new weapons (bronze, iron, gunpowder) from within a vaguely stable regime, then you’re set up to be suddenly and easily conquered later on.
When those earlier empires expanded, after conquering a region (with the associated rape, muder and pillaging of course), they would assimilate them into the empire, and often the conquered people benefited long-term… the Romans were quite well known for developing infrastructure as they went.

When Africa was later invaded, there was no interest in the making the people citizens, they were instead taken as slaves en masse, instead of developing the countries for the people there, they set up forts and colonies that excluded indiginous people and tried to keep them oppressed.

Recovering after the colonia era and actually stabilizing and adapting to a modern world economy takes time, some countries in Africa are doing fine, a few are even thriving.