Background and Objectives: The vedolizumab clinical decision support tool (VDZ-CDST) was developed to predict treatment outcomes in inflammatory bowel disease (IBD). While validated in clinical trial and consortium settings, its real-world performance remains less clear. The aim of our study was to evaluate the predictive value of pre-treatment CDST stratification for clinical and endoscopic outcomes and treatment persistence in real-world VDZ-treated IBD patients. Materials and Methods: We conducted a retrospective analysis of consecutive IBD patients initiating vedolizumab therapy, stratified by CDST risk groups. Clinical remission (CR) and corticosteroid-free remission (CSFR) at weeks 14 and 52 were assessed using PRO-2 in both Crohn’s disease (CD) and ulcerative colitis (UC). Endoscopic outcomes and treatment persistence were also evaluated. Results: 129 IBD patients, 57 with CD and 72 with UC, treated with vedolizumab were retrospectively stratified according to VDZ-CDST. In CD at week 52 the differences in CSFR between CDST groups were statistically significant (p = 0.04). A statistically significant association (p < 0.001) was also observed between CDST groups and endoscopic activity (EA) at follow-up endoscopy. In the low-probability group 69.2% showed persistent EA, whereas in the high-probability group 68.8% achieved endoscopic remission (ER). We also found significant differences (p = 0.004 and p < 0.001, respectively) in treatment persistence between CDST groups in CD. VDZ discontinuation rates were 76.9%, 28.6%, and 6.3% in the low-, intermediate-, and high-response groups, respectively. In UC, no predictive association was observed for either clinical or endoscopic outcomes nor treatment persistence; however, we observed relatively high remission rates despite CDST-based stratification. Conclusions: Although the VDZ-CDST failed to predict CR measured by PRO-2 in real-world IBD patients, it demonstrated meaningful associations with long-term CSFR, endoscopic outcomes and treatment persistence in Crohn’s disease. These findings support its role as a supportive tool in therapeutic decision-making, particularly when objective outcomes such as mucosal healing are prioritized. Prospective multicentre studies incorporating biomarkers and pharmacokinetic data are needed to refine VDZ-CDST for broader clinical application.