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Abstract Background The patient-centred medical home (PCMH) is a model of team-based primary care that is patient-centred, coordinated, accessible, and focused on quality and safety. In response to substantial population growth and increasing demand on existing primary care services, the Institute for Urban Indigenous Health (IUIH) developed the IUIH System of Care-2 (ISoC2), based on an international Indigenous-led PCMH. ISoC2 was piloted at an urban Aboriginal and Torres Strait Islander Community-Controlled Health Service in South-East Queensland between 2019–2020, with further adaptations made to ensure its cultural and clinical relevance to local Aboriginal and Torres Strait Islander people. Little is known on the implementation and impact of PCMH in the Australian Indigenous primary care setting. Changes in implementation process measures and outcomes relating to engagement and quality-of-care are described here. Methods De-identified routinely collected data extracted from electronic health records for clients regularly attending the service were examined to assess pre-post implementation changes relevant to the study. Process measures included enrolment in PCMH team-based care, and outcome measures included engagement with the health service, continuity-of-care and clinical outcomes. Results The number of regular clients within the health service increased from 1,186 pre implementation to 1,606 post implementation; representing a small decrease as a proportion of the services’ catchment population (38.5 to 37.6%). In clients assigned to a care team (60% by end 2020), care was more evenly distributed between providers, with an increased proportion of services provided by the Aboriginal and Torres Strait Islander Health Worker (16–17% versus 10–11%). Post-implementation, 41% of clients had continuity-of-care with their assigned care team, while total, preventive and chronic disease services were comparable pre- and post-implementation. Screening for absolute cardiovascular disease risk improved, although there were no changes in clinical outcomes. Conclusions The increase in the number of regular clients assigned to a team and their even distribution of care among care team members provides empirical evidence that the service is transforming to a PCMH. Despite a complex transformation process compounded by the COVID-19 pandemic, levels of service delivery and quality remained relatively stable, with some improvements in risk factor screening.