Exposure to phthalate/DINCH metabolites can induce human reproductive toxicity, however, their endocrine-disrupting mechanisms are not fully elucidated. To investigate the association between concentrations of phthalate/DINCH metabolites, serum kisspeptin, and reproductive hormones among European teenagers from three of the HBM4EU Aligned Studies. In 733 Belgian (FLEHS IV study), Slovak (PCB cohort follow-up), and Spanish (BEA study) teenagers, ten phthalate and two DINCH metabolites were measured in urine by high-performance liquid chromatography-tandem mass spectrometry. Serum kisspeptin (kiss54) protein, follicle-stimulating hormone (FSH), total testosterone (TT), estradiol (E2), and sex hormone-binding globulin (SHBG) levels were measured by immunosorbent assays. Free Androgen Index (FAI) was calculated as a proxy of free testosterone. Adjusted sex-stratified linear regression models for individual studies, mixed effect models (LME) accounting for random effects for pooled studies, and g-computation and Bayesian kernel machine regression (BKMR) models for the phthalate/DINCH mixture were performed. The LME suggested that each IQR increase in ln-transformed levels of several phthalates was associated with lower kisspeptin MnBP: %change (95%CI): −2.8 (−4.2;-0.4); MEHP: −1.4 (−3.4,0.2) and higher FSH ∑DINP: 11.8 (−0.6;25.1) levels in females from pooled studies. G-computation showed that the phthalates/DINCH mixture was associated with lower kisspeptin −4.28 (−8.07;-0.34) and higher FSH 22.13 (0.5;48.4) also in females; BKMR showed similar although non-significant pattern. In males, higher phthalates metabolites MEHP: −12.22 (−21.09;-1.18); oxo-MEHP: −12.73 (−22.34;-1.93) were associated with lower TT and FAI, although higher DINCH OH-MINCH: 16.31 (6.23;27.35), cx-MINCH: 16.80 (7.03;27.46), ∑DINCH: 17.37 (7.26;29.74) were associated with higher TT levels. No mixture associations were found in males. We observed sex-specific associations between urinary concentrations of phthalate/DINCH metabolites and the panel of selected effect biomarkers (kisspeptin and reproductive hormones). This suggests that exposure to phthalates would be associated with changes in kisspeptin levels, which would affect the HPG axis and thus influence reproductive health. However, further research is needed, particularly for phthalate replacements such as DINCH. Display omitted •Phthalate/DINCH metabolites concentrations were assessed in 733 European teenagers.•Phthalate metabolites showed associations with lower TT levels in males teenagers.•DINCH metabolites showed associations with higher TT levels in males teenagers.•Phthalate/DINCH and its mixture were associated with lower kisspeptin levels in females.