Background: Mindfulness-based programs are increasingly used as a part of integrated treatment for inflammatory bowel disease (IBD). However, the majority of research has been quantitative with limited qualitative exploration of patients’ experiences of mindfulness programs and no studies among adolescents and young adults with IBD. Furthermore, there has been a paucity of research exploring the role of common psychotherapy and group factors within mindfulness programs. Objective: This study aims to explore the experiences of adolescents and young adults with IBD and depression who completed a mindfulness-based cognitive therapy (MBCT) group program, as well as the role of therapeutic alliance, group affiliation, and other common psychotherapy and group factors. Methods: This mixed methods qualitative study, nested within a randomized controlled trial (RCT) of MBCT for adolescents and young adults with IBD, will obtain qualitative data from focus groups and open-ended survey questions. The study aims to conduct three to four focus groups with 6-8 participants in each group. It will employ data and investigator triangulation as well as thematic analysis of the qualitative data. Results: The study was approved by the Mater Hospital Human Research Ethics Committee and recruitment commenced in May 2019; study completion is anticipated by early 2020. Conclusions: The study will contribute to the assessment of acceptability and feasibility of the MBCT program for adolescents and young adults with IBD. It will also elucidate the role of previously unexplored common psychotherapy and group factors within mindfulness training and help inform the design of a future large-scale RCT of MBCT in this cohort.