Providing universal health coverage (UHC) through better maternal, neonatal, child and adolescent health (MNCAH) can benefit both parties through North–South research collaborations. This paper describes lessons learned from bringing together early career researchers, tutors, consultants and mentors from the United Kingdom, Kenya, and South Africa to work in multi-disciplinary teams in a capacity-building workshop in Johannesburg, co-ordinated by senior researchers from the three partner countries. We recruited early career researchers and research users from a range of sectors and institutions in the participating countries and offered networking sessions, plenary lectures, group activities and discussions. To encourage bonding and accommodate cross-cultural and cross-disciplinary partners, we asked participants to respond to questions relating to research priorities and interventions in order to allocate them into multidisciplinary and cross-country teams. A follow up meeting took place in London six months later. Over the five day initial workshop, discussions informed the development of four draft research proposals. Intellectual collaboration, friendship and respect were engendered to sustain future collaborations, and we were able to identify factors which might assist capacity-building funders and organizers in future. This was a modestly funded brief intervention, with a follow-up made possible through the careful stewardship of resources and volunteerism. Having low and middle-income countries in the driving seat was a major benefit but not without logistic and financial challenges. Lessons learned and follow-up are described along with recommendations for future funding of partnerships schemes.