Aim: To determine whether participation in the continuous quality improvement (CQI) Audit and Best Practice for Chronic Disease programme improved care and outcomes for Indigenous children. Methods: Data were collected from 59 Australian primary health-care centres providing services to Indigenous people and participating in the programme (February 2008 and December 2013). Indigenous children aged less than 2 years and centres that completed three or more consecutive annual audits within the 6-year study period were included. Crude and adjusted logistic generalised estimating equation models were used to examine the effect of year of audit on the delivery of care. Odds ratio (OR) and 95% confidence interval (CI) were calculated. Outcomes were related to age-relevant health issues, including prevention and early intervention. These included administrative, health check, anticipatory guidance and specific health issues. Results: During the audit period, there were 2360 files from 59 centres. Those that had a recall recorded, improved from 84 to 95% (OR 2.44, 95% CI 1.44–4.11). Hearing assessments improved from 52 to 89% (OR 1.37, 95% CI 1.22–1.54). Improvement in anticipatory guidance, treatment and follow-up of medical conditions was almost universal. Conclusion: We documented significant improvements in quality of care of Indigenous children. Outcomes and their corresponding treatment and follow-ups improved over time. This appears to be related to services participating in annual CQI activities. However, these services may be more committed to CQI than others and therefore possibly better performing.