Background: Inflammatory bowel disease (IBD) frequently manifests at a young age, during the peak fertility years. Understanding the risks of negative pregnancy outcomes associated with IBD is crucial for effective pregnancy management and support. Additionally, it is essential to provide patients with the necessary knowledge to make informed choices and foster their confidence in navigating pregnancy while maintaining effective disease management. Although IBD frequently appears during the peak fertility years, knowledge about managing pregnancy in the context of IBD remains limited and often inaccurate among both physicians and patients. Our study aims to assess the complications occurring during pregnancy in patients with IBD, considering the level of disease activity, and to evaluate the standard of care provided to patients with chronic inflammatory conditions through a cohort analysis. Methods: Patients with IBD who had children were included in this single-center mixed-method (retrospective and prospective) study. Clinical data, disease progression, course of pregnancy, and complications were examined in women. Outcomes for children of men with IBD were also analyzed. To supplement the data, a survey addressing various pregnancy-related topics, including all patients from the university outpatient clinic for IBD, was conducted over a period of six months. Results: A total of 410 patients were screened retrospectively between 2010 and 2021. In total, 134 patients who had children were included in the study: 51.4% (n = 69) had Crohn’s disease, 44% (n = 59) had ulcerative colitis, and 4.6% (n = 6) had unclassified inflammatory bowel disease. Of the women, 85% (n = 34) were in remission for at least three months before pregnancy, 14.6% (n = 6) experienced an acute flare-up during pregnancy, and 10.3% (n = 4) and 7.7% (n = 3) had active disease at the time of delivery and during breastfeeding, respectively. Patients with IBD who were in remission before pregnancy did not experience a higher risk of pregnancy complications (no cases of pre-eclampsia or placental abruption were reported in this group). However, the rates of gestational diabetes and fever during pregnancy were 10% for those in remission, compared to 25% for those with active disease. Conclusions: Patients with IBD in remission did not present an increased risk of pregnancy complications. However, our survey indicates that those with active disease at conception were more likely to experience complications such as gestational diabetes and fever. These findings underscore the importance of adequate patient education regarding the safety of various IBD medications during pregnancy in order to avoid pregnancy-related complications.