Inflammatory bowel disease (IBD), encompassing ulcerative colitis and Crohn’s disease, poses challenges for treatment in some patients resistant to conventional and biologic therapies. “Mucosal healing,” the complete regeneration of damaged intestinal tissue, is crucial for improving prognosis. Organoid-based regenerative medicine, utilizing hematopoietic stem cells (HSCs), mesenchymal stem cells (MSCs), and recently discovered intestinal stem cells (ISCs), shows promise. ISCs can be cultured as organoids in vitro, and studies using mice colitis models demonstrate their ability to engraft onto colitic ulcers, reconstruct crypt-villus structures, and potentially reduce the risk of colitis-associated cancers. Endoscopy-assisted transplantation of organoids emerges as a potential alternative therapy for refractory IBD patients, offering hope for improved long-term outcomes.