<p>The use of digitized biometric methods to certify citizenship has increased in Africa. The embrace of the new biometric ID systems has been justified to ensure inclusive development, especially among marginalised groups. Paradoxically, the emergent ID systems further exacerbate existing institutionalized and social exclusions. Evincing this proposition, this research focuses on the second or third-generation non-pastoral Fulani and their descendants at Agogo in the southern part of Ghana. It critically analyses the Fulanis exclusionary and discriminatory experiences during the Ghana Card and voter ID registration. Using a qualitative case-study methodology, the findings illuminate how institutional discrimination (through bureaucratic discretionary power) and politicization of citizenship impact exclusions and bureaucratized processes of citizen registration and certification. The exclusionary experiences of the Fulani are tied to the idea of <i>indigeneity</i>, a colonially constructed and exclusionary political marker of a supposed ‘real Ghanaian’. Thus, indigeneity is integral to regimes and infrastructure of Ghanaian citizenship and specifically underpin the Ghana Card and the voter ID that socially sort, classify and categorize differentiated citizenship. This work argues that, in the context of SDG 16.9 (identity for all) and desirability for biometric ID systems to ensure inclusivity and enhance subalterns’ engagement in society, the Ghana card and voter ID in attempt to certify citizens, reproduce and consolidate existing exclusions, especially indigeneity-based and ethnicized differentiation of citizens. Thus, the nature of exclusionary tendencies does not emanate solely from the biometric identification infrastructure but rather its institutionalization with an existing exclusionary citizenship regime.</p>