Abstract Objective Low levels of bilirubin have recently been associated with obesity, diabetes mellitus, and metabolic syndrome. Here, we hypothesized that serum bilirubin levels might be already altered in overweight asymptomatic middle-aged individuals before full development of the metabolic syndrome. Methods Healthy nonsmoking adults aged 25–49 (64 women and 32 men) participated in this cross-sectional study. All participants who reported stable weight within the last three months underwent standard anthropomorphological measurements of body composition, blood pressure measurements, aerobic and anaerobic capabilities assessment, dietary intake evaluation, and fasting serological measurements of total and direct bilirubin, glucose, insulin, triglycerides, total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, and C-reactive protein. Participants were divided into normal-weight and overweight groups. Linear correlation and multiple regression analyses were used to examine the association of serum bilirubin levels with all metabolic syndrome risk factor changes. Results Serum bilirubin levels were lower in overweight healthy individuals of both sexes, and were negatively associated with abdominal obesity, insulin resistance, fasting glucose, fasting insulin, fasting triglycerides, total cholesterol, low-density lipoprotein cholesterol, and C-reactive protein levels but positively associated with aerobic body capabilities. Conclusion Our findings suggest that serum bilirubin levels have the potential to be employed as an early biomarker for indicating asymptomatic individuals at increased risk of developing metabolic syndrome.