Background Information is limited for the benefits of physical activity (PA) in preschoolers. Previous research using accelerometer-assessed PA may be affected for multicollinearity issues.

Objectives This study investigated the cross-sectional and prospective associations of sedentary behaviour (SB) and PA with body composition and physical fitness using compositional data analysis.

Methods Baseline PA and SB were collected in 4-year-old (n = 315) using wrist-worn GT3X+ during seven 24 h-periods. Body composition (air-displacement plethysmography) and physical fitness (PREFIT test battery) were assessed at baseline and at the 12-month follow-up.

Results Increasing vigorous PA at expenses of lower-intensity behaviours for 4-year-old was associated with body composition and physical fitness at cross-sectional and longitudinal levels. For example, reallocating 15 min/day from lower intensities to vigorous PA at baseline was associated with higher fat-free mass index (+0.45 kg/m2, 95% confidence intervals [CI]: 0.18–0.72 kg/m2), higher upper-body strength (+0.6 kg, 95% CI: 0.1–1.19 kg), higher lower-body strength (+8 cm, 95% CI: 3–13 cm), and shorter time in completing the motor fitness test (−0.4 s, 95% CI: −0.82 to [−0.01] s) at the 12-month follow-up. Pairwise reallocations of time indicated that the behaviour replaced was not relevant, as long as vigorous PA was increased.

Conclusions More time in vigorous PA may imply short- and long-term benefits on body composition and physical fitness in preschoolers. These findings using compositional data analysis corroborate our previously published results using isotemporal substitution models.