In developing nations, the implementation of Foundational Identity Systems (FIDS) has optimised service delivery and inclusive economic growth. Cross-border e-government will gain traction as developing countries increasingly look to identity federation and trustworthy interoperability through FIDS for the identification and authentication of identity holders. Despite this potential, the interoperability of FIDS in the African identity ecosystem has not been well-studied. Among the difficulties in this situation are the intricate internal political dynamics that have led to weak institutions, suggesting that FIDS could be used for political purposes; additionally, citizens’ or identity holders’ habitual low trust in the government raises concerns about data security and privacy protection. Similarly, vendor lock-in, cross-system compatibility, and ambiguous legislative rules for data exchange are other concerns. Interoperability is fundamentally necessary as a precondition for e-government services and serves as the foundation for the best possible service delivery in the areas of social security, education, and finance, as well as gender equality as demonstrated by the European Union (EU). Moreover, the integration of cross-border FIDS and an ecosystem of effective data governance will be created by unified data sharing via an interoperable identity system. Thus, in this study, we point to the challenges, opportunities, and requirements for cross-border interoperability in an African setting. Furthermore, we investigated current interoperability solutions such as the EU’s eIDAS and Estonian X-Road and proposed an approach for scoping requirements to achieve a fully functional interoperable identity ecosystem in the African setting. Our findings show that interoperability in the African identity ecosystem is essential for expanding the scope of e-government throughout the continent and for bolstering the smooth authentication and verification of identity holders for inclusive economic growth.