The launch of the third edition of the National guide to preventive health assessment for Aboriginal and Torres Strait Islander people in March 2018 heralds a renewed commitment to improving the delivery of preventive care, and should reinvigorate discussions on the effectiveness of Indigenous-specific health assessments and how best to implement them. A substantial body of evidence on adherence to guideline-recommended care has been generated through a research-based continuous quality improvement (CQI) initiative conducted between 2010 and 2014. The research, which involved clinical audits of more than 17000 client records and 119 systems assessments relating to preventive care in 137 Indigenous primary healthcare centres across Australia, shows that a structured CQI program can improve the delivery of preventive health assessments and use of evidence-based guidelines. However, program implementation has also seen the emergence of new challenges. This paper reflects on four major lessons from this collaborative program of applied research that will lead to more effective delivery of preventive care.