(1) Background: Applied health services research (AHSR) relies upon coordination across multiple organizational boundaries. Our aim was to understand how competing organizational and professional goals enhance or impede the conduct of high quality AHSR. (2) Methods: A qualitative study was conducted in two local health care systems in the UK, linked to a feasibility trial of a clinic-based intervention in secondary care. Data collection involved 24 semi-structured interviews with research managers, clinical research staff, health professionals, and patients. (3) Results: This study required a dynamic network of interactions between heterogeneous health and social care stakeholders, each characterized by differing ways of organizing activities which constitute their core functions; cultures of collaboration and interaction and understanding of what research involves and how it contributes to patient care. These interrelated factors compounded the occupational and organizational boundaries that hindered communication and coordination. (4) Conclusions: Despite the strategic development of multiple organizations to foster inter-professional collaboration, the competing goals of research and clinical practice can impede the conduct of high quality AHSR. To remedy this requires the alignment and streamlining of organizational goals, so that all agencies involved in AHSR develop a shared understanding and mutual respect for the progress of evidence-based medicine and the complex and often nuanced environments in which it is created and practiced.
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