BackgroundThis study sought to determine how institutional environments, including values, policies, and their implementation, shape inequities in scientific career progression for women and men, and their disadvantages in relation to their multiple social identities in sub-Saharan Africa (SSA). The findings are drawn from a wider research study that was aimed at gaining an in-depth understanding of the barriers and enablers of gender-equitable scientific career progression for researchers in SSA. This was nested within the context of the Developing Excellence in Leadership, Training and Science in Africa (DELTAS Africa) programme—a health-based scientific research capacity-strengthening initiative.MethodsThe study adopted an exploratory qualitative cross-sectional study design. In-depth interviews (IDIs) with trainees/research fellows at various career stages supported and/or affiliated to three purposively selected DELTAS Africa Research Consortia were the main method of data collection. In addition, key informant interviews (KIIs) with consortia research leaders/directors, co-investigators, and the consortia management team were also conducted to corroborate information gathered from the IDIs, and also to provide additional insights on the drivers of intersectional gender-inequitable career progression. In total, 58 IDIs (32 female and 26 male) and 20 KIIs (4 female and 16 male) were conducted. The interviews were carried out in English between May and December 2018. The data were analysed inductively based on emergent themes.ResultsThree interrelated themes were identified: first, characterization of the institutional environment as highly complex and competitive with regard to advancement opportunities and funding structure; second, inequitable access to support systems within institutions; third, informal rules—everyday experiences of negative practices and culture at the workplace, characterized by negative stereotypical attitudes, gender biases, sexual harassment, and bullying and intimidation.ConclusionsWe contend that understanding and addressing the social power relations at the meso-institutional environment and macro-level contexts could benefit career progression of both female and male researchers by improving work culture and practices, resource allocation, and better rules and policies, thus fostering positive avenues for systemic and structural policy changes.