Background: We followed polycystic ovary syndrome (PCOS) women with metabolic syndrome (MS) over a six-year treatment period and evaluated the influence of PCOS phenotypes on MS and on the risk for type 2 diabetes mellitus (T2DM). Methods: This was an observational study of 457 PCOS women, whose demographic, clinical, hormonal, and metabolic data underwent analysis. The PCOS women were divided into four groups per NIH recommendations. Results: After a follow-up of a mean of six years (1–20 years), 310 patients were selected to assess the development of T2DM and MS. The clinical and biochemical parameters, along with the Rotterdam phenotypes, were evaluated. Data were analyzed using Student’s t- and the Pearson chi-square tests for data variation and group proportions, respectively. Additionally, multivariate analysis was applied to evaluate the effect of PCOS phenotypes on the risk for MS and T2DM. Patients of the four PCOS phenotypes did not differ in age, body mass index, total testosterone, insulin resistance, and dyslipidemia, but phenotype A patients showed the highest risk for T2DM. A decrease in androgen levels was not followed by an improved metabolic profile; instead, there was a significant increase in the number of T2DM cases. Conclusion: Phenotype A women are at the highest risk for type 2 diabetes mellitus.