The following are challenges that ECOWAS has faced in its operation.
- Political instability in member states. Countries like Nigeria and Ghana have witnessed Military coups. Civil wars have been fought in Sierra Leone, Liberia and Ivory Coast. These have been a hindrance to cooperation.
- Nationalistic issues. Most member states give priority to their own domestic issues at the expense of the organization.
- Language barrier. Countries in West Africa inherited the languages of their former colonial masters. The problem in communication has hindered the efficient operation of the organization.
- Infrastructural problems. The state of roads, railway, and communication linkages are poor. This has hampered the economic progress of member states.
- Ideological differences. The leaders of the member states view each other with suspicion and mistrust due to differences in ideologies.
- Lack of uniform currency. Each country has its own currency. This creates a problem of rates of exchange thus hindering trade.
- Foreign interference. The presence of Israeli and French soldiers in Cote D’Ivoire was viewed suspiciously by guinea.
- Border closures. For example between Ghana and Togo and between Burkina Faso and Mali.