Environmental factors play a role in increasing or decreasing the risk of metabolic syndrome (MetS) in adolescents. We analyzed the impact of physical activity (PA), dietary habits, and mental and socioeconomic status on MetS prevalence in 2143 (boys: 1113, girls: 1030, age: 13–18 years) Korean middle- and high-school students. Metabolically healthy obesity and metabolically unhealthy normal weight were also evaluated. MetS occurred in 215 participants (10.0%), and boys had a higher MetS rate than girls. There was no significant difference in alcohol consumption and smoking experience between individuals with and those without MetS. The odds ratio (OR) for high-school students was 1.33 (95%CI, 1.001–1.789, p = 0.043) times that of middle-school students. Depression, low aerobic PA, and high sedentary time increased the ORs to 1.64 (95%CI, 1.059–2.539, p = 0.020), 1.52 (95%CI, 1.092–2.203, p = 0.003), and 1.86 (95%CI, 1.342–2.587, p < 0.001), respectively. Higher energy intake and low weekly breakfast consumption frequency yielded ORs of 1.46 (95%CI, 1.046–2.555, p = 0.025) and 1.70 (95%CI, 1.244–2.339, p = 0.011), respectively. Strength training, stress, suicidal ideation, dining out frequency, and household income did not impact MetS prevalence. Despite obesity, MetS decreased by 29.7% with high aerobic PA and 37.9% with high weekly breakfast consumption frequency. In conclusion, MetS risk was higher for men, individuals with depression, and high-school students. Low aerobic activity, high calorie intake, and low weekly breakfast consumption frequency increased MetS risk. Despite obesity, high aerobic activity, low sedentary time, and breakfast consumption was associated with lower MetS risk.