Background The benefits of using qualitative research in trials (QRT) have been demonstrated and it is commonly used. However, the prevalence of QRT and issues with its conduct have been highlighted. Underpinned by a pragmatic approach, this study aimed to explore the use of QRT and identify factors that influence its implementation and reporting. Methods A convergent mixed methods design which included five components 1) a systematic review of 1,492 registered trials that report using qualitative research (1999-2016), 2) a critical review of 2,343 publications reporting QRT (2011-2017), 3) a narrative synthesis which involved the thematic analysis of 23 publications (2011-2020), 4) a case study of three trials which used qualitative research. The case study included nine interviews with members of the case study trial teams as well as 149 trial documents, and 5) the development and piloting of two quality appraisal checklists for QRT reporting. Findings The use of QRT has increased over time, but overall usage remains low. Use is limited to trials investigating behavioural interventions, those conducted in rich Western countries and in trials in co-morbidity conditions, oncology, and mental health. Overall reporting quality for QRT appears to be good but is variable with some areas of reporting being poorer. Engagement with QRT depends on people understanding it and seeing its value. Embedding qualitative researchers within the trial team, good collaborative relationships, consideration of the needs of all trial components and how these relate to each other and being flexible can help to overcome methodological tensions and ensure successful QRT. Conclusion Researchers and other stakeholders involved in trials need to recognise the benefits that QRT can bring and consider its use in a wide range of health areas, countries and in trials evaluating all forms of interventions. Further recommendations for the planning, conduct and reporting QRT are provided.