A distinction is often made between research into the efficacy of a treatment, i.e. whether it can be shown to work under ideal conditions, and research into the effectiveness of a treatment, i.e. whether it can be shown to work within a routine health service or usual clinical practice. The purpose of this article is to use descriptive information collected from personnel on the implementation and evaluation of a psychological intervention as a way to highlight some of the challenges faced when conducting research within everyday clinical settings. A psychological intervention for low self-esteem was evaluated within a standard inpatient ward for dual diagnosis patients. Descriptive information was collected from interviews to identify the challenges encountered during the research process. A qualitative analysis of interview content was undertaken to identify the major themes. Personnel described a range of patient variables, staff characteristics and organizational factors that hindered the research process. A detailed account of these factors along with potential solutions that can facilitate research in clinical settings is provided. Conducting research within clinical settings requires considerable planning and monitoring throughout the whole research process. Particular attention should be given to the impact of patient characteristics, staff variables and organizational context when designing and implementing research protocols. The value of this type of research within everyday clinical settings has significant implications for improving patient treatment and outcomes across psychiatric services.