Responding to complex needs calls for integrating care across providers, settings and sectors. Among models to improve integrated care, case management demonstrates a good evidence base of facilitating the appropriate delivery of healthcare services. Since case management is a complex, multi component intervention, with its component parts interacting in a non-linear manner, effectiveness is largely influenced by the context in which the intervention is implemented. This paper discusses how to respond to implementation challenges to evaluating complex interventions for patients with complex needs. Building on the example of case management, we suggest that documenting innovation effectiveness remains important, but that evaluation needs to include theory-based and systems perspectives. We also suggest that implementation science needs to be part of intervention design while engaging stakeholders to define the most relevant research questions and implementation effectiveness, to optimize successful implementation and sustainability.