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Abstract Background Noncommunicable diseases (NCDs) predominantly affect adults, but pathophysiological changes begin decades earlier, as a continuum, with initial events apparent in adolescence. Hence, early identification and intervention are crucial for the prevention and management of NCDs. We investigated the complex network of socioeconomic, behavioral, and metabolic factors associated with the presence of NCD in Brazilian adolescents. Methods We conducted a cross-sectional study nested within the São Luís segment of the Ribeirão Preto, Pelotas, and São Luís (RPS) cohort’s consortium, focusing on 18–19-year-olds (n = 2515). Data were collected prospectively, from which we constructed a complex network with NCD-related factors/indicators as nodes and their co-occurrences as edges. General and sex-based models analyzed: socioeconomic status, behavioral (smoking, alcohol, and other drugs use, unhealthy diet, poor sleep, physical inactivity), and metabolic factors (overweight/obesity, elevated blood pressure, poor lipid profile). We also looked for NCDs in adolescence like asthma, abnormal spirometry, depression, suicide risk, and poor oral health. The network was characterized by degree, betweenness, eigenvector, local transitivity, Shannon entropy, and cluster coefficient. Results The adolescents had an average age of 18.3 years, 52.3% were female and 47.7% male. 99.8% of them have a diet rich in free sugars, 15% are overweight/obese and 72.3% had an elevated TyG index. High free sugar emerged as the central hub, followed by high TyG index (an early marker of insulin resistance) and low socioeconomic class. In males, low fiber intake and a high triglycerides/HDL ratio highlighted cardiometabolic concerns; in females, sedentary behavior and poor sleep marked metabolic and psychological challenges, along with caries in both sexes. Conclusions Our findings provide insights into central health challenges during adolescence, such as high free sugars, insulin resistance, and low socioeconomic indicators, suggesting that interventions targeted at these central hubs could have a significant impact on their NCD network.