Polycystic ovary syndrome (PCOS) is associated with increased risks for certain metabolic disorders such as insulin resistance, non-alcoholic fatty liver disease (NAFLD), and suppressed ovarian follicular development. This study aimed to examine whether soya isoflavones (ISF) mitigate these PCOS-associated metabolic disorders in a rat model. Weanling Sprague-Dawley female rats were randomly divided into 6 groups and were treated with either 0 or 83 µg/day dihydrotestosterone (DHT) to induce PCOS and fed diets containing 0, 0.5, or 1g ISF/kg diet for 8 weeks. DHT treatment increased food intake, body weight gain (BWG, p<0.001), percentage of primordial follicles (60% vs 50.9%, p<0.05), and accumulation of lipid droplets in the livers. It also elevated serum total cholesterol (TC), free cholesterol (FC), triglycerides, non-esterified fatty acids (NEFA), and leptin, and hepatic TC and NEFA. Additionally, DHT treatment reduced the percentage of primary follicles (13.8% vs 30.2%, p<0.05), ovary weight, and length (p<0.001), as well as insulin sensitivity (p<0.01) compared to the Control. ISF intake at 1g/kg reduced BWG, serum TC, FC, NEFA, leptin, and hepatic triglycerides and DHT-induced insulin resistance (p<0.01). ISF intake at both levels decreased DHT-induced lipid droplet accumulation in the livers, and changes in the percentages of primordial and primary follicles. Dietary soya ISF alleviated DHT-induced BWG, insulin resistance, and hepatic lipid droplet accumulation, as well as suppressed ovarian follicular development. This suggests that consumption of soya foods or ISF supplements may be beneficial for the individuals with PCOS, mitigating the associated metabolic disorders such as diabetes and NAFLD.