Background Excessive body fat is the leading cause of many metabolic disorders. Therefore, assessing levels of body fat associated with risk of disease in specific populations is crucial. The present study aimed to identify optimal cut-off values of body fat composition including total body fat, body fat percentage, visceral fat, and trunk fat, in order to predict metabolic risk in the Qatari population. Methods This cross-sectional study was based on Qatar Biobank data of 2407 Qatari adults (1269 male and 1138 female) aged 21–70 years old. Individuals’ height, weight and body fat percentage were obtained. Blood test data including lipid profile, blood glucose and HbA1c data were also obtained. The area under the curve was calculated using ROC analysis to obtain the body fat percentage associated with risk of disease. Results The cut-off points for total fat for those aged < 40 were 34.0 kg, and for those aged ≥40 were 30.7 kg and 35.6 kg in men and women, respectively. The cut-off for body fat percent for those aged < 40 were 35.1 and 45.1%, and for those aged ≥40 were 34.8 and 46.3% in men and women, respectively. The cut-off points for trunk fat percent for those aged < 40 were 19.5 and 22.4%, and for those aged ≥40 were 21.6 and 23.4% in men and women, respectively. The cut-off points for visceral fat percent for those aged < 40 were 1.4 and 1.0%, and for those aged ≥40 were 1.9 and 1.4% in men and women, respectively. Conclusion This study established Qatari adult-specific cut-off values of body fat for different age and gender groups.