The etiology of Inflammatory Bowel Disease (IBD) is not fully understood but is believed to involve a dysregulated immune response to intestinal microbiota in genetically susceptible individuals. Individuals with IBD are at increased risk of infections due to immunosuppressive treatments, comorbidities, and advanced age. Current evidence indicates that IBD patients are not at higher risk of SARS-CoV-2 infection compared to the general population, though the risk of severe outcomes remains debated. A retrospective observational study was conducted using Apulian regional health data from 2020 to 2022. This study included 1029 IBD patients and 3075 controls, matched by age and sex. COVID-19 incidence, hospitalization, and case fatality rates were analyzed alongside vaccination coverage. No significant differences in COVID-19 incidence (IRR = 0.97), hospitalization (p = 0.218), or lethality (p = 0.271) were evidenced between IBD patients and the general population. Vaccination rates were high in both groups, with slightly higher uptake in IBD patients. Multivariate analysis identified age and male sex as risk factors for severe COVID-19 outcomes, while vaccination significantly reduced hospitalization and lethality risks. IBD patients in Apulia do not have an increased risk of COVID-19 infection or severe outcomes compared to the general population. Vaccination is crucial in protecting IBD patients, and ongoing efforts to promote vaccination within this population are essential. Future research should focus on the impact of specific IBD treatments on COVID-19 outcomes and the long-term effectiveness of vaccines.