Background: Excess adiposity is one of the main risk factors for the development of cardiovascular and metabolic diseases. The purpose of this study is to compare cardiometabolic risk factors in eutrophic adolescents with a high body fat percentage (%BF) with eutrophic adolescents with adequate %BF and those with excess weight and %BF. Methods: Cross-sectional study with 1043 adolescents. This study presented power equal to 99.75%. Body fat and anthropometric, clinical and biochemical indicators were evaluated. Participants were grouped according to body composition classified by body mass index (BMI) and body fat percentage. Statistical analyses were performed using R software version 4.0.2, adopting a significance level of 5%. The Mann–Whitney test, principal components analysis and logistic regression were performed. Results: It was observed that the SG was more similar to GC2 than to GC1 for both sexes, demonstrating that there was a greater similarity between these groups in relation to the evaluated factors. Higher values for TC, SBP and TG were associated with the SG when the CG1 was used as reference, controlled for sex and age. Likewise, higher TC values and lower levels of SBP, TG and LDL were related to SG when the CG2 was used as reference. Conclusion: Body fat assessment is more effective in predicting risk factors and cardiometabolic diseases than BMI alone.