Introduction: Long-term sequelae following acute SARS-CoV-2 infection appear to be common in patients with inflammatory bowel diseases (IBDs). Methods: We examined the frequency and characteristics of post-COVID-symptoms in patients with IBD (IBD-COVID), comparing them to two control cohorts: infected household members of the IBD-COVID patients without IBD (CONT-COVID) and IBD patients without SARS-COV-2 infection (IBD-no-COVID). A questionnaire for the retrospective documentation of possible post-COVID-19 symptoms was distributed to patients and controls from eight referral centers. Results: The 319 IBD-COVID, 108 CONT-COVID, and the 221 IBD-no-COVID patients were similar in terms of sex, age, and comorbidities. The occurrence and duration of fatigue in the IBD-COVID cohort correlated with IBD activity. Other complaints such as reduced cognitive performance (p < 0.05) and sleeping disorders (p < 0.05) were even more common in IBD-COVID patients. Persistent hematochezia (p < 0.001), abdominal pain (p < 0.005), diarrhea (p < 0.0001), and anal problems (p < 0.01) were more often in the IBD-COVID patients than in the CONT-COVID cohort. Furthermore, typical IBD-associated symptoms persist for a longer period after an infection. Frequency of post-COVID complaints is higher in IBD patients compared to controls. After infection, the number of outpatient consultations increased in IBD-COVID patients (7.8% vs. 10.9%, p = 0.008). Conclusion: Fatigue, cognitive impairment, and sleep disturbances are more prevalent among IBD-COVID than CONT-COVID patients. Furthermore, typical IBD-associated symptoms persist for a longer period after an infection. Frequency of post-COVID complaints is higher in IBD patients compared to controls. Tight control of IBD activity could be a suitable tool to avoid post-COVID problems.