Abstract Background Sustainable Development Goal (SDG) 17 focuses on North/South partnerships for sustainable development. Literature on research partnerships and capacity -building often neglects how these processes are carried out in practice, their social impacts and participants’ subjective experiences. Recognizing the increasingly global dimensions of Higher Education Institutions, the University Development and Innovation – Africa project (UDI-A) was designed to train lecturers and administrative staff of Angolan and Mozambican Universities through collaborations with European institutions, aiming at strengthening African academic and social landscapes through knowledge translation and dissemination. This paper examines potential outcomes of UDI-A on participants’ academic pathways, investigating the conflict between different imaginaries of capacity-building and partnerships, focusing on how Angolan and Mozambican health sciences researchers experience international collaborations. Methods Semi-structured interviews were conducted with seven health academics, as well as a focus group discussion involving all participants. These were recorded, fully transcribed, anonymized and coded to identify common themes. A consent form was signed by all participants. Results and discussion UDI-A was considered innovative, fostering the improvement of pedagogical skills and increasing social entrepreneurship activities. Participants arrived with a specific institutional mandate and believed that the training received should be incorporated into institutional practices to “modernize” these specific Portuguese speaking African Universities and the health sector. The institutional mechanisms put in place to attain this goal, Centres for Academic Development and Innovation (“CADIs”), were considered potential research and development hubs and drivers of academic and societal transformation. Nevertheless, participants shared a sense of asymmetry (infrastructural, financial, in terms of access to information) between them and European trainers. Although this asymmetry was the underlying basis of this capacity-building project, they argued that UDI-A did not fully acknowledge their local contexts, compromising the prospective development of partnerships in the health field. Conclusions More attention should be devoted to understanding how participants experience capacity building processes, integrating the diversity of their aspirations and perceptions into subsequent phases of the project, requiring the development of methodological innovations to increase the impact of these programs.