This paper examined effects of two interventions on cardiorespiratory fitness and motor skills, and whether these effects are influenced by baseline levels, and dose of moderate-to-vigorous physical activity (MVPA) during the intervention. A cluster randomized controlled trial was implemented in 22 schools (n = 891; 9.2 ± 07 years). Intervention groups received aerobic or cognitively engaging exercise (14-weeks, four lessons per week). Control groups followed their regular physical education programme. Cardiorespiratory fitness, motor skills and MVPA were assessed. Multilevel analysis showed no main effects on cardiorespiratory fitness and motor skills although the amount of MVPA was higher in the aerobic than in the cognitively engaging and control group. Intervention effects did not depend on baseline cardiorespiratory fitness and motor skills. Children with a higher dose of MVPA within the intervention groups had better cardiorespiratory fitness after both interventions and better motor skills after the cognitively engaging intervention. In conclusion, the interventions were not effective to enhance cardiorespiratory fitness and motor skills at a group level, possibly due to large individual differences and to a total dose of MVPA too low to find effects. However, the amount of MVPA is an important factor that influence the effectiveness of interventions.