Despite almost a century's research capacity strengthening in Africa, HIV/AIDS research has been dominated by high-income countries (HICs), illustrating broader inequalities in the global knowledge economy. The perpetuation of weak social science capacity in east Africa is analysed as part of a complex system with multiple causes at different socio-ecological levels. Furthermore, although primarily driven by HIC/ neo-colonialist interests, causes also stem from low-income countries (LICs), and individual actions reproduce macro-level structures. Most factors link to global economic inequalities, and the extraction of data and intellectual capacity from east Africa operates akin to Dependency Theory, but this is exacerbated by African governments. At the meso-level, HIC institutions prioritise revenue and publications over strengthening LIC research capacity, whatever their rhetoric, while serious impediments exist in east African institutions. At the micro-level, HIC researchers perpetuate inequalities through, e.g., prioritising output, maintaining dependency, and choosing HIC rather than LIC conferences and journals. Multiple responses are needed, particularly at the macro-level, especially long-term, tailored funding. Meso-level responses include meritocratic career structures and institutional research consultancies. Individual HIC researchers should, ideally, prioritise training and mentoring, but this risks career advancement. Above all, honesty is required about motives and conflicting interests, at institutional and individual levels.