Background: Epidemiological studies have suggested a possible correlation between nutritional factors and gastrointestinal diseases. Methods: A case–control study was designed in order to investigate if functional foods consumption and Mediterranean diet adherence have a positive effect in ulcerative colitis, Crohn’s disease, irritable bowel syndrome, and gastroesophageal reflux disease. In total, 142 patients (cases) and 147 gender-matched healthy people (controls) participated in the study. Functional food consumption was screened by using a Food Frequency Questionnaire based on the NHANES study, while Mediterranean diet adoption was evaluated by a 14-item Med Diet Assessment tool based on the PREDIMED study. The statistical analysis was performed with SPSS-22. Results: In the previous 2–3 years, the controls had more frequently consumed some categories (probiotics, prebiotics-enriched, and low-fat foods) and some kinds of functional foods (mountain tea, berries, pomegranate, oats, mastics, turmeric, soybeans, and raisins) compared to the cases (p < 0.05). Healthy people were more adherent to the Mediterranean diet than patients (p < 0.05). A multifactor analysis showed that the augmented score of the Mediterranean diet and the augmented consumption of categories and kinds of functional foods were protective factors in the appearance of gastrointestinal diseases. Conclusions: More studies should be conducted in order to further investigate the possible association between specific food components and gastrointestinal diseases’ pathophysiology.