Post-marketing surveillance is essential to evaluate the risk/benefit profile of drugs; however, pharmacovigilance studies comparing persistence and safety of biologic therapies in patients with inflammatory bowel disease (IBD) are scant. The aim of this study was to prospectively investigate persistence together with safety profiles of biologics in a cohort of patients diagnosed with Crohn’s Disease (CD) or ulcerative colitis (UC) followed by the IBD unit of Messina and treated with infliximab (IFX), adalimumab (ADA), golimumab (GOL), vedolizumab (VED), and ustekinumab (UST) from 2017 through 2021. Descriptive and treatment persistence analyses with predictors for discontinuation and occurrence of adverse drug reactions (ADRs) were performed. A total of 675 IBD patients were enrolled. A higher persistence rate was noted for UST and ADA in the first year (83.8% and 83.1%, respectively) and for IFX in the fifth year of treatment (58.1%). GOL, VED, and UST—all used as second/third-line therapies—seemed to have a higher risk of non-persistence than IFX (in order HR: 2.19; CI 95%: 1.33–3.61, 1.45; 1.04–2.04, 2.25; 1.25–4.07) as well as switchers and those who had at least one ADR (18.1; 13.22–24.68 and 1.55; 1.20–1.99, respectively). The reported ADRs, which were generally mild–moderate, were largely known. However, real-world data should be implemented to further study undetected safety concerns, including risk of malignancy.