Capsule retention is a rare but clinically significant complication of video capsule endoscopy (VCE), particularly in patients with refractory celiac disease. We report the case of a 42-year-old man with type II refractory celiac disease who developed jejunal capsule retention after VCE despite a negative magnetic resonance enterography (MRE). Conservative treatment with prednisone and laxatives resulted in spontaneous capsule passage after 30 days, avoiding endoscopic or surgical retrieval. This case highlights the importance of careful patient selection, pre-procedural risk assessment, and individualized management of capsule retention in inflammatory small bowel disease.