In this study, we explored how free play and scaffolding practices in Early Childhood Education and Care (ECEC) related to children's externalising problems both in ECEC and later in school. Furthermore, we aimed to reduce the knowledge gap of whether these relations depended on children's differences in emotional temperament. We used structural equation modelling to analyse data from 7421 children from the Norwegian Mother, Father and Child Cohort Study. Results indicated that more free play associated with less externalising problems in ECEC for children in general. For children with higher emotionality, more free play related to increased externalising problems in school. Scaffolding in ECEC was not associated with externalising problems, but moderated the longitudinal association of free play for children with higher emotionality. All children benefited from free play in ECEC for their concurrent mental health. However, for children with higher emotionality, more free play in ECEC might be a risk factor for reduced mental health in school, where there is less free play than in ECEC. More scaffolding in combination with free play in ECEC can reduce this risk. Further research should address the content of play and scaffolding practices in more detail.