Traditionally under international law, States controlled the right to the management and decision-making of international organizations by conferring powers on the plenary organ composed of government representatives who had to approve every important decision unanimously. However, the non-permanent nature of plenary bodies necessitated the creation of the Secretariat to oversee the day to day administration of these intergovernmental organizations. But the transformation of international organizations into autonomous supranational entities makes the study of its institutions difficult. The power of international organizations is demonstrated by recent events like Brexit, Trump’s inward-looking and a host of protectionist policies of states that try to detach themselves from the influence of international organizations. Consequently, this paper examines the role of the ECOWAS Commission in the implementation of community objectives. It focuses mainly on the role of the secretariat in the transformation of the ECOWAS regime from economic integration into human rights protection.