PurposePhysical activity (PA) has positive effects on children’s development. Particularly in childhood, PA plays an important role for children’s motor skills. The objective of this study was to examine the influence of the intervention program “Join the Healthy Boat” on motor abilities of primary school children.MethodsThe baseline measurements of this longitudinal intervention study with an intervention (IG) and control group (CG) were taken at the beginning of the school year 2010/2011 (T1) and follow up measurements in 2011/2012 (T2). Efficacy of the intervention on children’s motor abilities was assessed using a standardized and validated test battery (Dordel-Koch-Test). An exploratory factor analysis was performed in order to reduce dimensions. Differences between CG and IG were examined using analysis of covariance adjusting for age, gender, BMI percentiles and baseline data.ResultsChildren in the IG showed an significant improvement in the conditional skills (F(1,1571) = 5.20, p ≤ 0.02) and less decline in flexibility (F(1,1715) = 6.68, p ≤ 0.01) than children in the CG. Additionally, positive differences in the flexibility tests were ascertained for girls, F(1,839) = 100.88, p ≤ 0.02).ConclusionThe study showed that an intervention that aims to increase PA affects certain parts of children’s motor skills significantly. This was achieved without any extra PA lessons at school but with a low-threshold intervention integrated into the daily school routine.