Background: Globally, increasing numbers of higher education institutions (HEIs) in non-English-speaking countries have adopted English as a medium of instruction (EMI), because of the perception that this provides opportunities to attract high calibre students and academic staff, and engage with the international research community. We report an evaluation of a North-South-South collaboration to develop health research capacity in Democratic Republic of Congo (DRC) by establishing a postgraduate programme in nutritional epidemiology at the Kinshasa School of Public Health (KSPH), where English was adopted as the medium of instruction. We report experiences and perceptions of stakeholders, facilitators and students about using EMI.Methods: In-depth qualitative interviews were conducted between October-December 2019 among purposively sampled stakeholders (8), facilitators (11) and students (12) involved in the programme from all three partner institutions (University of Kinshasa; University of KwaZulu-Natal, South-Africa; University of Bergen, Norway). Interviews were conducted in participants’ language of preference (English or French), audio-recorded, transcribed verbatim and translated into English when required. Analysis employed a thematic approach. Results: Most participants viewed EMI positively, reporting that studying in English created opportunities to access relevant literature, improve interactions with the scientific community and advance their careers. As a result of adopting EMI, some students had opportunities to present research findings at international conferences, and publish their research in English. English-speaking researchers from partner institutions were able to participate in supervision of students’ research. However, inadequate English competency, particularly among students, was challenging, with some students reporting being unable to understand or interact in class, which negatively affected their academic performance. Further, EMI created barriers at KSPH among academic staff who were not proficient in English, leading to lack of integration with other postgraduate programmes. Participants suggested additional English language support for EMI.Conclusion: Partnerships between HEIs are a powerful tool to develop research capacity in low income countries and improve research outputs and evidence-based decision-making. EMI was able to develop the common ground required to establish a collaboration between HEIs where several languages were spoken. However, investing in wide-ranging supports to develop English proficiency is essential to ensure that challenges do not outweigh the benefits.