Purpose To evaluate the perceptions of undergraduates and mentors on the appropriateness, acceptability, and feasibility of a mentored seed-grant (micro-research) by Health Professions Education Partnership Initiative - Transforming Ugandan Institutions Training Against HIV/AIDS (HEPI-TUITAH) program on HIV training in Uganda. Methods We conducted a cross-sectional descriptive qualitative study with focus groups, on HIV micro-research training, with undergraduate health professions students and faculty mentors across three partner institutions in rural Uganda. Results A total of 24 students and 13 mentors (5–8 per group) took part in the focus group discussions. Most participants stated that the HEPI-TUITAH micro-research program was acceptable, appropriate and feasible for health professions undergraduate students. The interprofessional education approach of bringing together students from different programs and years of study was valuable especially for peer mentorship. There was a need to provide for institution-based training in addition to the centrally organized training for the benefit of all the team members. Participants also noted a need for the program to find a way of providing the students with data collection experience even with the COVID-19 pandemic situation. Conclusion The HEPI-TUITAH micro-research program was perceived as acceptable, appropriate, and feasible for health professions undergraduate students. It also promoted teamwork and academic collaboration. Provision for institution-based micro-research training activities and data collection experiences for the undergraduate students even during the COVID-19 pandemic would make the program more valuable. The lessons learnt will be applied to future training cohorts to optimize program impact and may be useful for similar programs in other settings.