This study aimed to examine the effect of the ToyBox-intervention, a kindergarten-based, family-involved intervention on different components of motor performance ability in children aged 3 to 6 years. We also assessed the influence of demographic and anthropometric, social and behavioural factors on effects of the intervention. The intervention and control were cluster-randomized (2:1 ratio) and children's anthropometry and two motor test items covering coordination (jumping from side to side, JSS) and strength (standing long jump, SLJ) were assessed before and after the intervention over one year. 1,293 children with different socio-economic status from 45 kindergartens in Germany were included (intervention, n=863; control, n=430). The intervention group showed a better improvement in JSS over time (P=0.01) and tended to improve better in SLJ (P=0.08). The intervention was more effective in boys than in girls with respect to SLJ (P=0.01). Children aged <4.5 years did not show a significant benefit of the intervention while older children improved (SLJ, P=0.004; JSS, P=0.04). The subgroup of children with low SES improved in JSS (P=0.0001) whether no significant changes were detectable in the subgroups with medium and high SES. The ToyBox-intervention improved specific components of motor performance ability in early childhood. Future programs should consider specific targeting of subgroups based on gender, age and SES.