Abstract Background Medical researchers in resource-constrained settings must make difficult moral decisions about the provision of ancillary care to participants where additional healthcare needs fall outside the scope of the research and are not provided for by the local healthcare system. We examined research stakeholder perceptions and experiences of ancillary care in biomedical research projects in Malawi. Methods We conducted 45 qualitative in-depth interviews with key research stakeholders: researchers, health officials, research ethics committee members, research participants and grants officers from international research funding organisations. Thematic analysis was used to analyse and interpret the findings. Findings All stakeholders perceived the provision of ancillary care to have potential health benefits to study participants in biomedical research. However, they also had concerns, particularly related to the absence of guidance to support it. Some suggested that consideration for ancillary care provision could be possible on a case-by-case basis but that most of the support from research projects should be directed towards strengthening the public health system, emphasising public good above individual or personal benefits. Some researchers and ethics committee members raised concerns about potential tensions in terms of funding, for example balancing study demands with addressing participants’ additional health needs. Conclusion Our findings highlight the complexities and gaps in the guidance around the provision of ancillary care in Malawi and other resource-constrained settings more generally. To promote the provision of ancillary care, we recommend that national and international guidelines for research ethics include specific recommendations for resource-constrained settings and specific types of research.