Polycystic ovary syndrome (PCOS) is the main endocrine disorder in women of reproductive age worldwide. This condition is often associated with various metabolic alterations that contribute to the development of metabolic syndrome (MetS). Recent research suggests that branched-chain amino acid (BCAA) dysregulation is observed in PCOS. This study aims to investigate the relationship between dietary patterns, body composition, metabolic analytes, and serum amino acid levels in Mexican women with PCOS. Utilizing a cross-sectional design, we found that both study groups, PCOS (n = 24) and PCOS + MetS (n = 21), exhibited increased relative fat mass and dietary habits characterized by high simple sugar intake and low protein consumption, correlating with levels of relative fat mass and leptin. Notably, serum concentrations of BCAAs and glutamic acid were significantly elevated in the PCOS + MetS group. Our findings suggest that a metabolic approach may enhance the prediction and management of MetS in women with PCOS, highlighting the importance of dietary interventions in this population.