Obesity is a recognized risk factor for the development of cardiometabolic outcomes. Therefore, it is essential to evaluate anthropometric and body composition indicators used for its diagnosis. This study aimed to assess the diagnostic performance of body fat percentage (BF%), fat mass index (FMI) and body mass index (BMI) for detecting cardiometabolic outcomes in adults. A cross-sectional study was conducted involving adults at 30 years of age from Pelotas, RS (n = 3517) and at 37–39 years from Ribeirão Preto, SP (n = 1696). Receiver operating characteristic (ROC) curves were used to determine the cut-off points for predicting cardiometabolic risk factors, including altered blood pressure, blood glucose, triglycerides, total cholesterol, low-density lipoprotein cholesterol (LDL-c), high-density lipoprotein cholesterol (HDDL-c), C-reactive protein and glycated hemoglobin. The cut-off points of BF% ranged from 25.2 to 27.8 in men and from 37.4 to 39.7 in women at 30 years, and from 26.1 to 27.8 in men and from 38.5 to 42.2 in women at 37–39 years. For FMI (kg/m2), the cut-off points ranged from 6.3 to 7.5 in men and from 9.5 to 10.8 in women at 30 years, and from 7.3 to 7.8 in men and from 10.2 to 12.2 in women at 37–39 years. The BMI cut-off points (kg/m2) ranged from 26.3 to 27.3 in men and from 25.4 to 27.2 in women at 30 years, and from 28.3 to 29.0 in men and from 27.2 to 29.6 in women at 37–39 years. The areas under the curve were similar for the three indicators, ranging from 0.523 to 0.746. BMI showed a performance similar to that of the body fat-based indicators in identifying cardiometabolic outcomes. The cut-off points of the three indicators showed acceptable discriminatory power in subjects with cardiometabolic risk factors.