For more than two decades countering jihadism and Islamist terrorism has been priority on the security agendas of African countries. The franchising of indigenous militant groups to established jihadist organisations like al-Qaeda and the Islamic State has been a global concern. What has been a phenomenon in both Western and Eastern Africa, is the failure of the states to counter these groups militarily, economically, and ideologically. The cases of Somalia, Nigeria and Mali depict this growing trend. Does al-Shabaab stand to exploit the recent turmoil in the Horn of Africa and the Middle East to stage a come-back in Somalia? Does the resurgence of Boko Haram and other emerging militant groups reinforce the calls for a separatist Islamic state in Nigeria? How does the shift in alliances in Mali affect the government’s counterterrorism efforts and how are the Islamist organisations responding?