Background Australians report consulting with a naturopaths or herbalists to improve their wellbeing, yet little is known about the associations between these consultations and the patients’ health behaviours. This cross-sectional study aimed to examine the relationship between health behaviour and consultations with naturopaths or herbalists in three age cohorts of Australian women. Methods Women aged 19–25 years, 31–36 years, and 62–67 years from the Australian Longitudinal Study on Women’s Health (ALSWH) were surveyed regarding smoking, alcohol or drug use, physical activity and dietary behaviour; and whether they consulted with naturopath/herbalists in the last 12 months. Associations were analysed using multivariable logistic regression. Results A total of 9151 (19–25 years), 8200 (31–36 years) and 11,344 (62–67 years) women were included in the analysis. Between 7.3 and 11.9% of women reported to have consulted with naturopaths/herbalists in the last 12 months. Women of all cohorts consulting with naturopath/herbalist were less likely to smoke (19-25 yrs.: Odds Ratio [OR] 0.61; 31–36 years: OR 0.58; 62–67 years: OR 0.29), more likely to report at least moderate levels of physical activity (19-25 yrs.: OR 1.41; 31–36 years: OR 1.34; 62–67 years: OR 1.34), and the use of vegetarian diets(19-25 yrs.: OR 1.40; 31–36 years: OR 1.77; 62–67 years: OR 2.28), compared to women not consulting with naturopaths/herbalists. Women consulting with naturopaths/herbalists however were also more likely to have used marijuana (19-25 yrs.: OR 1.18; 31–36 years: OR 1.42), or illicit drugs in the last 12 months (19-25 yrs.: OR 1.24; 31–36 years: OR 1.40). Conclusions Consultations with a naturopath or herbalist are associated with positive health behaviours that are protective of internationally important non-communicable diseases. Psychoactive drug use is also reported among women visiting a naturopath or herbalist. Further research is needed to understand the role naturopaths play in advising patients with regards to health and non-healthy behaviours.