Patients with inflammatory bowel disease (IBD) have a dysregulated immune system, being at high risk of opportunistic infections. Low vaccination rates hinder the prevention of such diseases. Therefore, we implemented an intervention to increase vaccination rates, and we aimed to evaluate the effect. We determined the change in professionals and the change in the vaccination rates after the intervention. A quasi-experimental study was carried out using data from 31 December 2016 to 31 December 2021. First, healthcare professionals specializing in IBD agreed on a vaccination protocol; then, this protocol was passed on to the professionals involved in vaccination. We evaluated the perception of knowledge, capacity, and intention to vaccinate patients with IBD among the professionals before and after the intervention with a survey. We also described the effectiveness of the intervention for already diagnosed patients and compared the vaccination rates between patients diagnosed prior to the intervention and newly diagnosed patients. The intervention resulted in an improved perception of knowledge, capacity, and intention to vaccinate patients with IBD among the professionals (p < 0.05). Moreover, during the post-intervention period, in the 315 patients, the vaccination rate increased for all immune-preventable diseases (p < 0.05). The professionals positively valued the intervention, and compliance with the recommended vaccination protocol in patients with IBD improved significantly.