Peace-through-health has emerged as a promising concept but with variable evidence of success. Cooptation of health initiatives in conflict is believed to be a major challenge undermining peacebuilding potential. We examine the role that existing power structures and health initiative characteristics play at various levels of a conflict in peacebuilding outcomes. Using the Syrian conflict as a case study, we assess healthcare initiatives’ characteristics and their peacebuilding tendencies accounting for power dynamics at the (1) state citizen, (2) interbelligerents and (3) intercommunity conflict levels, drawing on the WHO’s framework for health and peace initiatives. Healthcare interventions at state citizen and interbelligerent levels generally addressed combat-related and material-dependent health needs, relied on large-scale international funding and centralised governance structures, and bestowed credit to specific agencies with political implications. These characteristics made such initiatives prone to cooptation in conflict with limited peacebuilding capacity. Healthcare initiatives at the community level addressed more basic, service-dependent needs, had smaller budgets, relied on local organisations and distributed credit across stakeholders, making them less amenable to cooptation in the conflict with more propeace potential. A pilot peacebuilding health initiative designed to leverage these propeace attributes navigated the political environment, minimised cooptation and fostered community collaboration, resulting in peacebuilding potential. In summary, peacebuilding health initiatives are more likely to materialise at the community as compared with higher political levels. Further studies, accounting for conflict power structures, are needed to examine the effectiveness of such initiatives and identify methods that maximise their peacebuilding outcomes.