Evaluating integrated care innovations poses unique challenges due to their inherent complexity, contextual variability, and the interdependence of healthcare components. This chapter explores how these challenges can be addressed by integrating complexity into the evaluation design from the outset. We provide an overview of the full methodological toolbox of both interventional and observational designs and offer practical guidance on how to navigate the selection of appropriate methods. A structured decision tree supports researchers in aligning study design with the research question, context, and real-world implementation conditions. The chapter advocates for a pluralistic, context-sensitive approach that values methodological diversity over rigid adherence to traditional clinical trial models. Emphasis is placed on the importance of early and participatory evaluation planning, aligning study design with real-world conditions, and involving all relevant stakeholders from the outset. By adopting a flexible, interdisciplinary methodology, evaluations can produce actionable insights that inform policy, enhance implementation, and ultimately improve care delivery in complex healthcare systems.