In the study, 305 patients of both genders were enrolled and divided into three groups: obese (BMI > 30 kg/m), patients who were diagnosed type 2 diabetes mellitus (T2DM), and control, normal weight healthy volunteers. At least one of ten different phthalate metabolites was determined in the urine samples of 49.84% all enrolled participants. In the obese subgroup, the sum of all urinary phthalate metabolites was positively associated with TG levels (p = 0.031) together with derived TC/HDL and TG/HDL ratios (p = 0.023 and 0.015), respectively. Urinary MEP concentration was positively correlated with the HOMA-IR in T2DM subgroup (p = 0.016) while in the control subgroup, logMEP levels were negatively correlated with total cholesterol (p = 0.0051), and LDL serum levels (p = 0.0015), respectively. Also, in the control subgroup, positive linear correlations between urinary logMEP levels and TyG and TYG-BMI values (p = 0.028 and p = 0.027), respectively, were determined. Urinary MEHP levels were associated with glucose serum levels (p = 0.02) in T2DM subgroup, while in the control HDL values were negatively associated with logMEHP (p = 0.0035). Healthy volunteers exposed to phthalates had elevated AST levels in comparison to non-exposed ones (p = 0.023). In control subgroup, ALT and AST values were increased (p = 0.02 and p = 0.01, respectively) in MEP exposed while GGT levels were enhanced (p = 0.017) in MEHP exposed in comparison with non-exposed. Combined phthalates influence on glucose and lipid metabolism may increase the possibility for NAFLD and insulin resistance development among exposed individuals.