BACKGROUND: Global health research partnerships have been scrutinised for how they operate and criticised for perpetuating inequities. Guidance to inform fair partnership practice has proliferated and the movement to decolonise global health has added momentum for change. In light of this evolving context, we sought in this study to document contemporary experiences of partnership from the perspective of stakeholders in four sub-Saharan African research institutions. METHODS: We conducted qualitative interviews with 20 stakeholders at research institutions in four countries in anglophone eastern and southern Africa. Interview questions were informed by published guidance on equitable research partnerships. Data was analysed through an iterative process of inductive and deductive coding, supported by NVivo software. RESULTS: Early-career, mid-career and senior researchers and research administrators from four sub-Saharan African research institutions described wide-ranging experiences of partnership with high-income country collaborators. Existing guidelines for partnership provided good coverage of issues that participants described as being the key determinants of a healthy partnership, including mutual respect, role clarity and early involvement of all partners. However, there was almost no mention of guidelines being used to inform partnership practice. Participants considered the key benefits of partnership to be capacity strengthening and access to research funding. Meanwhile, participants continued to experience a range of well-documented inequities, including exclusion from agenda setting, study design, data analysis and authorship; and relationships that were exploitative and dominated by high-income country partners' interests. Participants also reported emerging issues where their institution had been the prime recipient of funds. These included high-income country partners being unwilling to accept a subordinate role and failing to comply with reporting requirements. CONCLUSIONS: Insights from stakeholders in four sub-Saharan African research institutions suggest that contemporary global health research partnerships generate considerable benefits but continue to exhibit longstanding inequities and reveal emerging tensions. Our findings suggest that long-term support targeted towards institutions and national research systems remains essential to fulfil the potential of research led from sub-Saharan Africa. High-income country stakeholders need to find new roles in partnerships and stakeholders from sub-Saharan Africa must continue to tackle challenges presented by the resource-constrained contexts in which they commonly operate.