Background and aim: Nutritional deficiencies are frequent in coeliac disease (CeD), mostly because of the nutritional deficits in gluten-free foods and because of wrong behaviors. We aimed to investigate the level of nutritional knowledge in a cohort of CeD patients in comparison with patients with inflammatory bowel disease (IBD) and healthy subjects. Materials and methods: We consecutively recruited CeD patients and matched-sex and -age IBD patients between April and December 2019 at the University Hospital of Padua outpatient clinic. Healthy subjects were also recruited from family and friends of the hospital staff. The CeD patients were asymptomatic on a gluten-free diet, whereas the IBD patients were in remission. All of the subjects completed the Moynihan validated questionnaire to measure their nutritional knowledge. Results: We included 96 CeD patients, 96 IBD patients, and 65 healthy controls. We found that CeD patients were less aware of nutritional recommendations compared with healthy subjects (HS), and were less able to identify nutrient sources compared with IBD patients and to choose healthy food compared with both groups. The Moynihan questionnaire mean total score was not significantly different between CeD and IBD groups (mean 22.5 ± 2.3 for CeD, 22.0 ± 2.2 for IBD), while it was statistically significantly worse in CeD compared with healthy subjects (mean 21.2 ± 2.3 for HS, p = 0.001). Conclusions: CeD patients tend to focus their diet on gluten avoidance, while IBD patients tend to follow a healthier diet, probably because they believe that diet plays a major role in regulating inflammation and, therefore, their symptoms. A dietitian consultation at CeD diagnosis is recommended.