The central aspect of this study is a set of reflections on the efficacy of soft operational research techniques in understanding the dynamics of a complex system such as intellectual disability (ID) care providers. Organizations providing services to ID patients are complex and have many interacting stakeholders with often different and competing interests. Understanding the causes for failures in complex systems is crucial for appreciating the multiple perspectives of the key stakeholders of the system. Knowing the factors that adversely affect delivery of a patient‐centred care by ID provider organizations offers the potential for identifying more effective resource‐allocation solutions. The authors suggest cognitive mapping as a starting point for system dynamics modelling of optimal resource‐allocation projects in ID care. The application of the method is illustrated via a case study in one of the ID care providers in the Netherlands. The paper discusses some of the practical implications of applying problem‐structuring methods that support gathering feedback from vulnerable service users and front‐line workers. The authors concluded that cognitive mapping technique can assist the management of healthcare organizations in strategic decision‐making. Copyright © 2013 John Wiley & Sons, Ltd.