Background/Objectives: Chronic gastrointestinal disorders often involve nutritional management strategies. On the one hand, inflammatory bowel disease (IBD) is a condition in which most of the patients experience frequent diet manipulation in order to obtain long term remission. On the other hand, for celiac disease (CelD), diet is the only known treatment strategy so far, requiring a life-long gluten-free diet. We aimed to evaluate the comparative food-related quality-of-life (FR-QoL) in light of these dietary interventions between these two conditions. Methods: This is a cross-sectional study, involving children aged 7–18 years diagnosed with IBD and CelD. Assessment of this aspect was performed using the self-reported FR-QoL 29 questionnaire. For CelD, the questionnaires were modified with “CelD” instead of “IBD”. Results: Fifty-one patients were included, 17 in each subgroup (Crohn’s disease (CD), ulcerative colitis (UC), and Celd). FR-QoL scores were negatively correlated with age at inclusion (Spearman’s ρ = −0.284, p = 0.04) and also with age at diagnosis (Spearman’s ρ = −0.291, p = 0.038). The scores were significantly lower in the CD group (64.1 ± 13.4) compared with CelD patients (78.6 ± 20.3), p = 0.036 and UC, p = 0.294. For the IBD group, the scores were not influenced by disease activity. Furthermore, we identified a negative significant correlation between anthropometric indices and FR-QoL scores. Conclusions: The burden of dietary intervention is highest for the CD patients, regardless of their disease activity when compared with UC and CelD patients, most probably because of the unpredictable course and fast response to dietary changes. Although it requires incessantly vigilant eating behavior, CelD has apparently become more “manageable” in recent years.