This article assessed security architecture for counter-insurgency against Boko Haram in the Lake Chad Basin (LCB). The paper diagnosed the impact of conflicting national interests of contributing nations on the performance of the Multinational Joint Task Force (MNJTF) as a regional security architecture in the LCB. Some scholars and analysts cite corruption, historical contradictions among LCB members, poor funding, and complex nature of the insurgency, as factors responsible for failure of counter-insurgency operations in the LCB. Others contend that resource geopolitics, linguistic differences, and hegemonic politics have impacted negatively on the capacity of the MNJTF to decimate terrorists in the region. This is a qualitative study that draws from the Fund for Peace, International Crisis Group (ICG), Lake Chad Basin Commission, the Armed Conflict Location and Event Data (ACLED), and research literature dealing with national interest and military alliances, while using content analysis to argue that conflicts in national interests, more than any other factor, have hampered the collaborative efforts of the Lake Chad Basin Commission (LCBC) and weakened the capacity of the MNJTF to engage in robust counterinsurgency against Boko Haram in the LCB.