Background and objectives: Despite the serious concerns of patients about the role of food in triggering or ameliorating their intestinal disease, there are few studies dealing with patients’ beliefs and practices regarding diet in inflammatory bowel disease (IBD). The aim of this study was to investigate how the disease affected the dietary habits of patients with IBD, and to assess if patients’ food restrictions were responsible for low bone mineralization. Materials and Methods: For this study, 90 consecutive patients referred for IBD were interviewed regarding their dietary habits. Demographic features and clinical characteristics potentially associated with the dietary habits were collected. A validated and self-administered survey questionnaire dealing with dietary habits and patients’ beliefs and perceptions regarding food was analyzed. Multivariate logistic regression analysis was performed in order to identify risk factors for dietary restrictions among participants and to evaluate the relationship between dietary restrictions and low bone mineral density (BMD). Results: Among the 63 (70%) patients who claimed a self-prescribed dietary restriction, 84% avoided dairy products. Significant risk factors (adjusted odds ratio (OR), 95% confidence interval (CI)) for the dietary restrictions were a younger age (p = 0.02), a higher level of education (p = 0.007), and a higher visceral sensitivity index (p = 0.009). Most (80%) of the patients displayed an inadequate calcium intake, and an abnormal result at dual-energy X-ray absorptiometry (DXA) scan accounting for low BMD was reported in 46 (51%) of them. Dietary restrictions (p = 0.03), and in particular avoiding dairy products (p = 0.001), were significant risk factors for a low BMD, along with female gender (p = 0.001), smoking (p = 0.04), and steroid abuse (p = 0.03). Almost all (86%) patients changed their diet after IBD diagnosis, as 8% believed that foods could have been a trigger for IBD and 37% that a proper diet was more important than drugs in controlling disease. Although 61% of the patients claimed to have received nutritional advice, 78% of the participants showed interest in receiving more. Conclusions: Dietary habits of IBD patients should be investigated by healthcare professionals as part of the routine visit. Clinicians are invited to provide nutritional recommendations to these patients in order to avoid unnecessary self-prescribed dietary restrictions.