Background The consequences for youth cardiometabolic risk might depend on whether sedentary time and physical activity are accumulated sporadically (in shorter bouts) or in a sustained pattern (in longer bouts). This study aimed to: 1) describe daily time-use compositions of youth, including time spent in shorter and longer bouts of sedentary behaviour and physical activity; and 2) examine associations between time-use compositions with cardiometabolic biomarkers.Methods Accelerometer and cardiometabolic biomarker data (adiposity, blood pressure, lipids) from 7–13 year olds (mean ± SD: 10.4 ± 1.7) from two Australian studies were pooled (complete cases adiposity n = 772). A time-use composition of nine components was formed using compositional data analysis: time in shorter and longer bouts of sedentary behaviour, light-, moderate- and vigorous-intensity physical activity, and “other time” (i.e., non-wear/sleep). Shorter and longer bouts of sedentary time were defined as < 5 and ≥ 5 min, respectively. Longer light-, moderate- and vigorous-intensity physical activity bouts were defined as ≥ 1 min. Linear regression models examined associations between overall time-use composition and cardiometabolic biomarkers. Then, associations between ratios of longer relative to shorter activity patterns, and each intensity relative to more intense activities and/or “other time”, with cardiometabolic biomarkers were derived.Results Confounder-adjusted models showed that the overall time-use composition was associated with zBMI, waist circumference, systolic blood pressure, high-density lipoprotein cholesterol, triglycerides, and a combined cardiometabolic risk score. Specifically, more time in longer relative to shorter bouts of light-intensity physical activity was associated with greater zBMI (β = 1.79, SE = 0.70, p = 0.010) and waist circumference (β = 17.28, SE = 4.87, p < 0.001). More time in longer relative to shorter bouts of vigorous-intensity physical activity was also associated with higher waist circumference (β = 2.54, SE = 1.14, p = 0.026). More relative time in total light- and vigorous-intensity physical activity (including longer and shorter bouts) was associated with lower waist circumference. In contrast, more relative time in sedentary behaviour and moderate-intensity physical activity was detrimental for waist circumference.Conclusions Accumulating physical activity in frequent short bursts may be beneficial for adiposity compared to engaging in the same amount of these intensities in longer bouts.Trial registration: 'Lifestyle Of Our Kids’ (ACTRN12615000066583 [23/01/2015]) and ‘Transform-Us!’ (ACTRN12609000715279 [19/08/2009], ISRCTN83725066 [30/06/2010]).