Background: The elevated risk of occupational infection such as tuberculosis among health workers in many countries raises the question of whether the quality of occupational health and safety (OHS) and infection prevention and control (IPC) can be improved by auditing. The objectives of this study were to measure (1) audited compliance of primary health-care facilities in South Africa with national standards for OHS and IPC, (2) change in compliance at reaudit three years after baseline, and (3) the inter-rater reliability of the audit. Methods: The study analyzed audits of 60 primary health-care facilities in the Western Cape Province of South Africa. Baseline external audits in the time period 2011–2012 were compared with follow-up internal audits in 2014–2015. Audits at 25 facilities that had both internal and external audits conducted in 2014/2015 were used to measure reliability. Results: At baseline, 25% of 60 facilities were “noncompliant” (audit score<50%), 48% “conditionally compliant” (score >50 < 80%), and only 27% “compliant” (score >80%). Overall, there was no significant improvement in compliance three years after baseline. Percentage agreement on specific items between internal and external audits ranged from 28% to 92% and kappa from -0.8 to 0.41 (poor to moderate). Conclusion Low baseline compliance with OHS–IPC measures and lack of improvement over three years reflect the difficulties of quality improvement in these domains. Low inter-rater reliability of the audit instrument undermines the audit process. Evidence-based investment of effort is required if repeat auditing is to contribute to occupational risk reduction for health workers.