BackgroundAddressing evidence-practice gaps in primary care remains a significant public health challenge and is likely to require action at different levels of the health system. Whilst Continuous Quality Improvement (CQI) is associated with improvements in overall delivery, little is known about delivery of different types of care processes, and their relative improvement during CQI.MethodsWe used data from over 15,000 clinical audit records of clients with Type 2 diabetes collected as part of a wide-scale CQI program implemented between 2005 and 2014 in 162 Aboriginal and Torres Strait Islander health centres. We abstracted data from clinical records on 15 service items recommended in clinical guidelines and categorised these items into five modes of care on the basis of the mechanism through which care is delivered: laboratory tests; generalist-delivered physical checks; specialist-delivered checks; education/counselling for nutrition and physical activity and education/counselling for high risk substance use. We calculated delivery for each patient for each of mode of care by determining the proportion of recommended services delivered for that mode. We used multilevel regression models to quantify variation attributable to health centre or client level factors and to identify factors associated with greater adherence to clinical guidelines for each mode of care.ResultsClients on average received 43 to 60 % of recommended care in 2005/6. Different modes of care showed different patterns of improvement. Generalist-delivered physical checks (delivered by a non-specialist) showed a steady year on year increase, delivery of laboratory tests showed improvement only in the later years of the study, and delivery of counselling/education interventions showed early improvement which then plateaued. Health centres participating in CQI had increased odds of top quartile service delivery for all modes compared to baseline, but effects differed by mode. Health centre factors explained 20–52 % of the variation across jurisdictions and health centres for different modes of care.ConclusionsLevels of adherence to clinical guidelines and patterns of improvement during participation in a CQI program differed for different modes of care. Policy and funding decisions may have had important effects on the level and nature of improvements achieved.