This study aimed to assess associations between chronotype and obesity-related indicators in a sample of Spanish adolescents. This cross-sectional study used data from The Eating Healthy and Daily Life Activities (EHDLA) Study, which included a representative sample of adolescents from Spain. A total of 820 adolescents (54.7% girls) aged 12-17 years were included in the analyses. The adolescents' chronotype was determined using the Morningness/Eveningness Scale in Children. Obesity-related indicators included body mass index, waist circumference, waist-to-height ratio, triceps and medial calf skinfolds, sum of skinfolds, and body fat percentage. Generalized linear models were used to examine the relationship between the Morningness-Eveningness score and chronotype status and the above-mentioned obesity-related indicators in adolescents. All analyses were adjusted for sex, age, socioeconomic status, sleep duration, physical activity, sedentary behaviour, adherence to the Mediterranean diet, and energy intake. The morningness chronotype was associated with higher abdominal obesity (odds ratio [OR] = 1.67, 95% confidence interval (CI) 1.12 to 2.50; p = 0.001), waist-to-height ratio (unstandardized beta coefficient [B] = 0.01, 95% CI 0.01 to 0.05; p = 0.029) and skinfold calves (B = 1.04 95% CI 0.24 to 1.94; p = 0.011), compared with the intermediate chronotype. Adolescents with a morningness chronotype may be more prone to abdominal obesity than their counterparts with an intermediate chronotype. Effective intervention-related approaches can be applied to those with a morningness chronotype.