Most actions targeting children's health behaviors have limited involvement of children in the development, potentially contributing to disappointing effectiveness. Therefore, in the 3-year "Kids in Action" study, 9- to 12-year-old children from a lower-socioeconomic neighborhood were involved as coresearchers in the development, implementation, and evaluation of actions targeting health behaviors. The current study describes the controlled trial that evaluated the effects on children's energy balance-related behaviors, physical fitness, and self-rated health, as well as experienced challenges and recommendations for future evaluations. Primary school children from the three highest grades of four intervention and four control schools were eligible for participation. Outcome measures assessed at baseline, and at 1- and 2-year follow-up were as follows: motor fitness by the MOPER test (N = 656, N = 485, N = 608, respectively), physical activity and sedentary behavior by accelerometry (N = 223, N = 149, N = 164, respectively), and consumption of sugar sweetened beverages and snacks and self-rated health by a questionnaire (N = 322, N = 281, N = 275, respectively). Mixed-model analyses were performed adjusted for clustering within schools and relevant confounders. Significant beneficial intervention effects were found on self-reported consumption of energy/sports drinks at T2 versus T0, and on total time and [greater than or equal to]5-minute bouts of moderate-to-vigorous physical activity at T1 versus T0. Significant adverse effects were found on "speed and agility" and "coordination and upper-limb speed." No other significant effects were found. The inconsistent intervention effects may be explained by the dynamic cohort and suboptimal outcome measures. We advise future studies with a similar approach to apply alternative evaluation designs, such as the delayed baseline design.