Physical education (PE) is acknowledged as a relevant context for holistic child and youth development promotion. However, interventional research mostly builds on individual theories focused on specific outcome domains. This study presents a multisport enriched PE intervention that capitalizes on the intersection of different theory-based approaches to motor, cognitive and socio-emotional skills development promotion. With a cross-over design, 181 fifth graders, coming from a past class-randomized trial of enriched or traditional PE in their 1st–3rd grade, were stratified (based on their previous PE experience) and class-randomized to multisport enriched PE or control group. They completed pre-post assessments in motor and sport skills, cool (inhibition, working memory) and hot (decision making) executive functions, prosocial (empathy, cooperation) and antisocial (quick-temperedness, disruptiveness) behaviors. Children in the enriched PE group showed advantages in motor and prosocial skills after the intervention, which were linked by a mediation path, and an interactive effect of past and actual PE experience on decision making but no differential effects on other variables. The results suggest that a PE intervention designed with an integrative theory base, although not allowing disentangling the contribution of individual components to its efficacy, may help pursue benefits in motor and non-motor domains relevant to whole-child development.