Background and objectives: Polycystic ovary syndrome (PCOS) is a common condition that affects fertility, body image and emotional wellbeing in women, as well as significantly increasing a woman’s likelihood of developing type 2 diabetes mellitus (T2DM) and other cardiovascular disease risk factors. The objective of this study was to assess how management of PCOS in an Aboriginal primary care setting aligns with national standards for diagnosis and screening of cardiometabolic risk and emotional wellbeing. Method: We conducted a retrospective clinical audit of 63 women who had PCOS listed as a diagnosis in their clinical record. Results: Most women (95%) were correctly diagnosed, the most common trigger being menstrual irregularity (83%). Screening for cardiometabolic complications and emotional wellbeing as recommended by the national guideline was applied inconsistently, including 38% of eligible women not being screened for T2DM in the previous 12 months, and no woman being formally screened for emotional wellbeing. Discussion of lifestyle management was nearly universal; most women (75%) were referred to a dietician, although a third did not attend their appointment. Discussion: Some components of recommended PCOS care were provided at high levels, including correct application of diagnostic criteria. However, PCOS management and screening for complications are being applied inconsistently in a population with high levels of cardiometabolic and emotional wellbeing risk.