BackgroundSignificant knowledge gaps exist in the functioning of institutional designs and organisational practices in purchasing within free healthcare schemes in low resource countries. The study provides evidence of the governance requirements to scale up strategic purchasing in free healthcare policies in Nigeria and other low-resource settings facing similar approaches.MethodsThe study was conducted at the Ministry of Health and in two health districts in Enugu State, Nigeria, using a qualitative case study design. Semi-structured interviews were conducted with 44 key health system actors (16 policymakers, 16 providers and 12 health facility committee leaders) purposively selected from the Ministry of Health and the two health districts. Data collection and analysis were guided by Siddiqi and colleagues’ health system governance framework. Data were analysed using a framework approach.ResultsThe key findings show that supportive governance practices in purchasing included systems to verify questionable provider claims, pay providers directly for services, compel providers to procure drugs centrally and track transfer of funds to providers. However, strategic vision was undermined by institutional conflicts, absence of purchaser-provider split and lack of selective contracting of providers. Benefit design was not based on stakeholder involvement. Rule of law was limited by delays in provider payment. Benefits and obligations to users were not transparent. The criteria and procedure for resource allocation were unclear. Some target beneficiaries seemed excluded from the scheme. Effectiveness and efficiency was constrained by poor adherence to purchasing rules. Accountability of purchasers and providers to users was weak. Intelligence and information is constrained by paper-based system. Rationing of free services by providers and users’ non-adherence to primary gate-keeping role hindered ethics.ConclusionWeak governance of purchasing function limits potential of FMCHP to contribute towards universal health coverage. Appropriate governance model for strengthening strategic purchasing in the FMCHP and possibly free healthcare interventions in other low-resource countries must pay attention to the creation of an autonomous purchasing agency, clear framework for selective contracting, stakeholder involvement, transparent benefit design, need-based resource allocation, efficient provider payment methods, stronger roles for citizens, enforcement of gatekeeping rules and use of data for decision-making.Electronic supplementary materialThe online version of this article (10.1186/s12913-018-3078-x) contains supplementary material, which is available to authorized users.