Background Polycystic Ovary Syndrome (PCOS) is a complex endocrine disorder characterised by irregular ovulation, hyperandrogenism and metabolic disturbances, while NAFLD is a hepatic condition marked by abnormal fat accumulation in the liver in the absence of significant alcohol intake. Polycystic Ovary Syndrome (PCOS) and Non-Alcoholic Fatty Liver Disease (NAFLD) frequently coexist due to shared metabolic and pathophysiological pathways. Ayurvedic literature describes dosha prakopa nidanas as contributors to metabolic dysfunction, but their relationship with modern metabolic comorbidities has not been extensively studied. Objective To assess the association between dosha-prakopa factors and the co-occurrence of PCOS and Grade 1 NAFLD. Methods An observational cross-sectional study was conducted on 30 female participants aged 17–35 years. Participants were divided into two groups: Group A (n = 15) with PCOS alone and Group B (n = 15) with PCOS and ultrasonography-confirmed Grade 1 NAFLD. A structured, validated questionnaire assessed exposure to dosha prakopa nidanas across three domains: ahara (dietary), vihara (lifestyle), and manasika (psychological). Associations were analysed using chi-square tests and odds ratios with 95% confidence intervals. Results Kapha prakopa showed a strong trend toward association with the coexistence of PCOS and NAFLD (OR 4.00; 95% CI 0.88–18.26; p = 0.144). The findings are consistent with Ayurvedic descriptions of Kapha’s heavy and oily qualities contributing to adipogenesis, insulin resistance, and hepatic fat accumulation. Conclusion Kapha imbalance may be a potential risk factor for the comorbidity of PCOS and NAFLD. By identifying Kapha imbalance as a potential risk factor, it validates classical Ayurvedic reference to the role of Medoroga and underscores the need for personalized, dosha-specific therapies.