Abstract Background At times of increasing pressure on emergency departments, and the need for research into different models of service delivery, little is known about how to recruit patients for qualitative research in emergency departments. We report from one study which aimed to collect evidence on patients’ experiences of attending emergency departments with different models of using general practitioners, but faced challenges in recruiting patients. This paper aims to identify and reflect on the challenges faced at all stages of patient recruitment, from identifying and inviting eligible patients, consenting them for participation and finally to engaging them in interviews, and make recommendations based on our learning. Methods A thematic analysis was carried out on field-notes taken during research visits and meeting minutes of discussions to review and improve patient recruitment throughout the study. Results The following factors influenced the success of patient recruitment in the emergency department setting: complicated or time-consuming electronic health record systems for identifying patients; narrow participant eligibility criteria; limited research nurse support; and lack of face-to-face communication between researchers and eligible patients. Conclusions This paper adds to the methodological evidence for improving patient recruitment in different settings, with a focus on qualitative research in emergency departments. Our findings have implications for future studies attempting to recruit patients in similar settings.