Individuals with inflammatory bowel diseases (IBDs) have an increased risk of developing psychiatric comorbidities, including eating disorders (EDs). We aimed to investigate the potential association between key disease characteristics, including psychological features, and the development of EDs in a clinical sample of adolescents with IBDs. We enrolled 52 adolescents with IBDs, 83% of whom were in clinical remission, and systematically collected additional information on disease duration, the total number of relapses, the use of steroids, and the number of hospital admissions. All participants completed a validated psychometric battery assessing psychological symptoms (Symptom Checklist-90-Revised, SCL-90-R), alexithymia (Toronto Alexithymia Scale-20, TAS-20), and ED symptomatology (Eating Disorders Inventory-3rd edition, EDI-3). About one in ten patients (9.6%) reported Eating Disorder Risk scores higher than the cut-off on the EDI-3 subscale, specifically addressing the risk of developing EDs. According to the EDI-3 scores, the risk of developing EDs directly correlated with the number of total relapses of IBDs (p < 0.05). The TAS-total scores also correlated with the number of total relapses (p < 0.01), as well as with the number of steroid cycles (p < 0.05), the number of hospital admissions (p < 0.05), and overall disease duration (p < 0.05). Our findings suggest that disease relapses increase the risk of developing both EDs and alexithymia in adolescents with IBDs. The recurrence of disease relapses should be identified and screened early on to prevent the onset of psychiatric disorders, including EDs. Research should be conducted on larger samples with different IBD phenotypes to further investigate the characteristics of patients with IBDs at risk of developing EDs.