INTRODUCTION: Primary health care organisations need to continuously reform to more effectively address current health challenges, particularly for vulnerable populations. There is growing evidence that optimal health service structures are essential for producing positive outcomes. AIM: To determine if there is an association between process of care indicators (PoCIs) for important young indigenous child health and social issues and: (i) primary health-care service and child characteristics; and (ii) organisational health service structures. METHODS: This was a cross-sectional study of 1554 clinical child health audits and associated system assessments from 74 primary care services from 2012 to 2014. Composite PoCIs were developed for social and emotional wellbeing, child neurodevelopment and anaemia. Crude and adjusted logistic regression models were fitted, clustering for health services. Odds ratios and 95% confidence intervals were derived. RESULTS: Overall, 32.0% (449) of records had a social and emotional wellbeing PoCI, 56.6% (791) had an anaemia PoCI and 49.3% (430) had a child neurodevelopment PoCI. Children aged 12-23 months were significantly more likely to receive all PoCIs compared to children aged 24-59 months. For every one point increase in assessment scores for team structure and function (aOR 1.14, 95% CI 1.01-1.27) and care planning (aOR 1.14, 95% CI 1.01-1.29) items, there was a 14% greater odds of a child having an anaemia PoCI. Social and emotional wellbeing and child neurodevelopment PoCIs were not associated with system assessment scores. DISCUSSION: Ensuring young indigenous children aged 24-59 months are receiving quality care for important social and health indicators is a priority. Processes of care and organisational systems in primary care services are important for the optimal management of anaemia in indigenous children.