Abstract Background Liver transplantation (LT) remains the only therapeutic option for patients with primary sclerosing cholangitis (PSC) who develop biliary tract complications or cirrhosis. Around 50-80% of PSC patients have IBD which represent phenotypically unique disease. Patients are prone to negative effects of complications of liver disease and immunosuppression, unpredictable course of both diseases and development of neoplasia. Patients are treated according to standard guidelines related to overall IBD population. Methods The study evaluates the IBD course and effects of therapy in PSC transplanted patients. In a period of 2005-October 2022 1453 patients had LT performed at University hospital Merkur, Zagreb, Croatia. 70 (4.8%) of them refers to complications of PSC. 46 (66%) of PSC patients were diagnosed with IBD, majority 43 (93.5%) before LT. Results As expected 36 (78.3%) had ulcerative colitis (UC) while 9 (19.6%) Crohns disease. 31 (70%) were males, median age 35 years (IQR 28-47). 35 (76.1%) patients had no IBD activity at LT, whereas 11 (23.9%) had continuously active IBD in follow up. 18 (51.4%) patients with remission at LT developed relapse (median time 536 days, IQR 371-1234) whereas other 17 (48.6%) have stable remission. Nine (19.6%) patients had malignant disease, 3 (6,5%) cholangiocelular carcinoma in explanted liver, 5 (10,9%) colorectal cancer (CRC) and 1 both tumors. Before LT 24 (52.2%) patients had no specific IBD treatment, whereas 8 (33.3%) were treated with aminosalicilates (AsA), 5 (10.9%) azathioprine (AzA), 6 (13.1%) glucocorticoids (GK) and 3 (6.5%) biologics. After LT 23 (50%) are treated with ASA, 12 (26.1%) AzA and 11 (23.9%) biological therapy (36.4% anti-TNF, 27,3% vedolizumab and 36,4% on multiple biologics). AsA as monotherapy is successful in 63.6% of treated patients, AzA in 50% and biologic therapy 27.3%, respectfully. Even though it did not reach statistical significance, more patients with relapse of IBD after LT are treated with AzA than in group of continuously active disease (33.3 vrs 9.1%) while this is opposite for biologic therapy (27.8 vrs 54.5%). 8 (17.4%) patients were treated with total colectomy, 2 before, 3 during and 3 after LT, 6 due to CRC and 2 intractable IBD. Regrading immunosuppression 42 (91.3%) are treated with tacrolimus, 4 (8.7%) with cyclosporine, 24 (52.2%) with mycophenolate mofetil and 11 (23.9%) prolonged GK. Conclusion Management of IBD in the context of PSC and LT setting is a major clinical challenge and specific guidelines are urgently needed. Since the effectiveness of standard therapy is possibly weaker with a high risk of cancer it is necessary to consider an earlier approach to colectomy.