Background A high quality modern diet is associated with reduced risk of metabolic disease and diabetes. However, it remains unclear whether the quality of predominantly traditional ethnic diets is associated with such conditions. Moreover, the relationship between dietary quality and microbiota, a potential mediator of metabolic disease, has not been studied. Objective We investigated the relationship of dietary quality of traditional ethnic diets in Indonesia with fasting blood glucose (FBG), HbA1c, and the number of fecal Bifidobacterium. Design A cross-sectional study was conducted in selected districts with predominantly animal- or plant-based traditional diets of West Sumatera and West Java provinces, respectively. A total of 240 apparently healthy women aged 19–50 years were randomly selected from 360 women screened by a cluster sampling design. Dietary quality was assessed by 2-day repeated 24-hour food recall, and scored using the Healthy Eating Index (HEI) 2010. FBG was quantified with the enzymatic colorimetric method, and HbA1c by using hexokinase and high-performance liquid chromatography, and total fecal Bifidobacterium by real-time quantitative polymerase chain reaction. Results The HEI scores of 99% of women were <51, indicating a low-quality diet. In adjusted multivariate regression, HEI was inversely associated with FBG (ß = -0.403; 95% CI = -0.789 to -0.016; p = 0.041) and HbA1c (ß = -0.018; 95% CI = -0.036 to 0.000; p = 0.048) but was not significantly associated with total levels of Bifidobacterium (ß = -0.007, p = 0.275). Bifidobacterium count was not significantly associated with either FBG or HbA1c levels. Conclusion Low dietary quality is clearly associated with risk of increased markers of blood glucose. However, any mediating role of Bifidobacterium between dietary quality and glucose outcomes was not apparent. Innovative interventions for healthy eating should be implemented to increase dietary quality of populations transitioning from predominantly traditional to modern diets, to reduce the risk of diabetes, especially in women.