Pediatric Inflammatory Bowel Disease (IBD) is a chronic illness where patients may undergo ostomy surgery. Medical decision-making (MDM) for ostomy surgery is complex for patients/families and multidisciplinary healthcare professionals (HCPs) alike, with current uncertainty about how multidisciplinary HCPs think about ostomy care to inform future interventions to facilitate equitable multidisciplinary care for patients. This study sought to understand pediatric IBD multidisciplinary HCPs' perceptions regarding ostomy-related MDM and education. Multidisciplinary HCPs (e.g., gastroenterology medical providers, social workers, surgeons, and ostomy nurses) participated in semi-structured focus groups. Focus group data underwent qualitative analysis to identify themes. Three multidisciplinary focus groups were conducted, with n = 12 participants across all groups. Qualitative analysis identified three main themes, including (1) HCP perceptions of ostomies, (2) Patient/family-related factors, and (3) Professional roles and collaboration challenges. Ostomy surgery in pediatric IBD requires complex multidisciplinary MDM and education. Perspectives of multidisciplinary HCPs identified patient, HCP, and systems factors that may impact MDM for ostomy surgery. This work highlights nuances in MDM and education in IBD, and the critical role of ongoing research and improved standardized processes to coordinate multidisciplinary ostomy-related MDM and education in this population.