Intersectoral action is advocated as a social practice that can effectively address health inequalities and related social issues. Existing knowledge provides insight into factors that may facilitate or hinder successful intersectoral action, but not much is known about how intersectoral action evolves and becomes embedded in local health policies. This is where this study aims to make its contribution, by adopting the multilevel perspective on transitions, which is increasingly used to study social innovation in sustainability transitions but has not yet been applied to public health and health promotion. Through this perspective, it was unravelled how intersectoral action between youth-care organizations and community sports clubs became embedded in local health policies of Rotterdam, a large city in the Netherlands. A single explorative case study was conducted based on content analysis of policy documents and 15 in-depth interviews with policy officers, managers and field workers operating in the fields of youth and sports in Rotterdam. The findings showed that intersectoral action between community organizations and policymakers evolves through congruent processes at different levels that changed institutional logics. Moreover, it emerged that policymakers and other actors that advocate novel social practices and act as boundary spanners can adopt multiple strategies to embed these practices in local health policy. The multi-level perspective adds value to earlier approaches to research intersectoral collaboration for health promotion as it allows to better capture the politics involved in the social innovation processes. However, further sharpening and more comprehensive application of transition concepts to study transitions in public health and health promotion is needed.