Abstract Background Between-person differences in sedentary patterns should be considered to understand the role of sedentary behavior (SB) in the development of childhood obesity. This study took a novel approach based on compositional data analysis to examine associations between SB patterns and adiposity and investigate differences in adiposity associated with time reallocation between time spent in sedentary bouts of different duration and physical activity. Methods An analysis of cross-sectional data was performed in 425 children aged 7–12 years (58% girls). Waking behaviors were assessed using ActiGraph GT3X accelerometer for seven consecutive days. Multi-frequency bioimpedance measurement was used to determine adiposity. Compositional regression models with robust estimators were used to analyze associations between sedentary patterns and adiposity markers. To examine differences in adiposity associated with time reallocation, we used the compositional isotemporal substitution model. Results Significantly higher fat mass percentage (FM%; βilr1 = 0.18; 95% CI: 0.01, 0.34; p = 0.040) and visceral adipose tissue (VAT; βilr1 = 0.37; 95% CI: 0.03, 0.71; p = 0.034) were associated with time spent in middle sedentary bouts in duration of 10–29 min (relative to remaining behaviors). No significant associations were found for short (