Our paper discusses various features of research excellence in Africa, framed within the context of African science granting councils and pan-African research excellence initiatives. Our survey, collecting responses from 106 researchers and research coordinators across Africa, highlights the diversity of opinions and preferences with regards to Africa-relevant dimensions of research excellence and related performance indicators. The results of the survey confirm that research excellence is a highly multidimensional concept. Our analysis shows how some of those dimensions can be operationalised into quantifiable indicators that may suit evidence-based policy discourses on research quality in Africa, as well as research performance assessments by African science granting councils. Our indicator case study, dealing with the top 1% most highly cited research publications, identifies several niches of international-level research excellence in the African continent while highlighting the role of scientific cooperation as a driving force. To gain a deeper understanding of research excellence in Africa, it is important to take into account the practical challenges faced by researchers and research funding agencies to align and reconcile socioeconomic interests with international notions of excellence and associated research performance indicators. African research excellence should be customised and contextualised in order to be responsive to African needs and circumstances.