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Background: UK local authorities are developing and implementing Whole Systems Approaches to childhood obesity to tackle persistent and complex health inequalities. However, there is a lack of research on the practical application of these approaches. This paper reports on findings of a study into the initial implementation of this approach in Dundee, Scotland. Study design/methods: We applied a mixed methods research design: 1) semi-structured interviews (n = 9) with partnership members; 2) training members as peer researchers to interview their wider networks; n = 17); 3) an online survey among wider stakeholders (n = 27); and 4) two action learning sets with decision makers. Interview data was analysed using thematic framework analysis and survey data was analysed using descriptive statistics. Results: Dundee stakeholders stated that they had good knowledge of childhood obesity prevention efforts, but their engagement with working groups around identified priority themes was still limited, due to a lack of awareness about existing structures and knowledge about sustainable, impactful strategies, which were not always well-aligned between key organisations. Conclusions: Our findings extend current literature on facilitators for Whole Systems Approaches in public health by highlighting that understanding of strategies and wider structures are crucial to build capacity and maintain engagement to address inequalities. We identified an ongoing need for targeted communication and diverse involvement opportunities for different stakeholder groups.