This essay explores transnational capacity building projects to highlight some of the structural and processual challenges in decolonizing institutional spaces and power structures. We offer a view from the Global North by drawing on our own experiences of such projects and argue that issues of coloniality in research capacity-building projects must be understood together with the concepts of dependency and universality of knowledge. Two examples are used to question who defines excellence and relevance at African universities. We conclude that many collaborative projects regard scientific knowledge and notions of excellence and standards as universal and therefore transferable without considering an African academic context. Moreover, the mobility of scholars leads to the mobility of knowledge and norms, which may emphasise the notion of universality. More research from the Global South is needed to illustrate how the paradoxes and dilemmas of international research collaboration and capacity building are experienced and understood