The unequal knowledge production and dissemination structure divides the world's academic system into a dominating mainstream circuit and a peripherical one, favoring the influence of certain communities in science and constituting the source of structural epistemic injustices. Several local and international initiatives have recently emerged to reduce regional inequalities and build alternative transnational publishing circuits. This paper studies alternative Journal Indexing Systems (JIS) and journal representation in alternative and traditional indexes. To do so, it focuses on the African publishing environment. First, it revises and compares the quality criteria of each database to explore the subjective nature of research quality. Then, the paper develops a methodology to compare journal coverage in different JIS and applies it to study African Journals Online, Scopus, and the Web of Science. It shows the coverage of the databases of African journals and their relative coverage in terms of countries, research areas, language, and geospatial focus. The results show the need for a situated notion of research quality and the biases of mainstream and alternative databases toward specific countries, research areas, and languages. The results presented here contribute to the ongoing conversation about diversity and inclusion in science and describe the current situation concerning the representation of African journals in three JIS. They can also be used to assess the limitations of our current bibliometric analysis and find ways to incorporate more inclusive data.