BACKGROUND: Despite being central to achieving improved population health outcomes, primary health centres in low- and middle-income settings continue to underperform. Little research exists to adequately explain how and why this is the case. This study aimed to test the relevance and usefulness of an adapted conceptual framework for improving our understanding of the mechanisms and causal pathways influencing primary health centre performance. METHODS: A theory-driven, case-study approach was adopted. Four Zambian health centres were purposefully selected with case data including health-care worker interviews (n = 60); patient interviews (n = 180); direct observation of facility operations (2 weeks/centre) and key informant interviews (n = 14). Data were analysed to understand how the performance of each site was influenced by the dynamic interactions between system 'hardware' and 'software' acting on mechanisms of accountability. FINDINGS: Structural constraints including limited resources created challenging service environments in which work overload and stockouts were common. Health workers' frustration with such conditions interacted with dissatisfaction with salary levels eroding service values and acting as a catalyst for different forms of absenteeism. Such behaviours exacerbated patient-provider ratios and increased the frequency of clinical and administrative shortcuts. Weak health information systems and lack of performance data undermined providers' answerability to their employer and clients, and a lack of effective sanctions undermined supervisors' ability to hold providers accountable for these transgressions. Weak answerability and enforceability contributed to a culture of impunity that masked and condoned weak service performance in all four sites. CONCLUSIONS: Health centre performance is influenced by mechanisms of accountability, which are in turn shaped by dynamic interactions between system hardware and system software. Our findings confirm the usefulness of combining Sheikh et al.'s (2011) hardware-software model with Brinkerhoff's (2004) typology of accountability to better understand how and why health centre micro-systems perform (or under-perform) under certain conditions.