This study contributes to the health policy debate on medical systems integration by describing and analysing the interactions between health-care users, indigenous healers, and the biomedical public health system, in the so far rarely documented case of post-conflict Burundi. We adopt a mixed-methods approach combining (1) data from an existing survey on access to health-care, with 6,690 individuals, and (2) original interviews and focus groups conducted in 2014 with 121 respondents, including indigenous healers, biomedical staff, and health-care users. The findings reveal pluralistic patterns of health-care seeking behaviour, which are not primarily based on economic convenience or level of education. Indigenous healers’ diagnosis is shown to revolve around the concept of ‘enemy’ and the need for protection against it. We suggest ways in which this category may intersect with the widespread experience of trauma following the civil conflict. Finally, we find that, while biomedical staff displays ambivalent attitudes towards healers, cross-referrals occasionally take place between healers and health centres. These findings are interpreted in light of the debate on health systems integration in Sub-Saharan Africa. In particular, we discuss policy options regarding healers’ accreditation, technical training, management of cross-referrals as well as of herb-drug interactions; and we emphasise healers’ psychological support role in helping communities deal with trauma. In this respect, we argue that the experience of conflict, and the experiences and conceptualizations of mental and physical illness, need to be taken into account when devising appropriate public or international health policy responses.