Despite their importance, federal grant systems often need more clarity regarding cost-effectiveness, lack of transparency, and slow feedback cycles. Sports funding systems aimed at improving child health and contributing to sustainable development goals are incredibly challenging due to their heterogeneity in stakeholders and regional aspects. Here, we analyze how we tackled these challenges in a transdisciplinary EU project in Austria, targeting the use of agent-based modeling for evidence-based policymaking in a co-creation process with policy stakeholders in the domain of federal sports grants to improve the health and well-being of children and youth. The initial and executed set of procedures is described, along with lessons learned during the project’s lifetime. These lessons derive a framework that provides an adapted set of processes, supporting methods, and critical decision points for an improved use of transdisciplinarity. In addition, the steps of the developed framework are combined with essential aspects of knowledge integration, following the main phases of the policy cycle and providing suggestions for required skills and competencies for capacity building concerning implementing the developed framework in the public sector. Our results show that the combination of transdisciplinarity, human-centered policymaking, and sports, supported by cutting-edge technologies such as agent-based modeling, can achieve significantly better results than a pure disciplinary approach and generate positive spill-over effects.