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Successful implementation of the Food & Fitness Initiative depended on community partners transforming complex systems to support healthy eating and active living, while addressing health equity. To apply systems thinking in diverse communities and in partnership with stakeholders who had differing levels of education and experience, we assembled a clear conceptual framework, an effective toolkit, and multiple opportunities to build capacity. This article describes the ways that we deployed systems thinking within the initiative, both collectively and at individual sites, and what we learned. Community partners offer advice to others who seek to transform complex systems.