Certain types of foods are common trigger for bowel symptoms such as abdominal discomfort or pain in patients with inflammatory bowel disease (IBD). But indiscriminate food exclusions from their diet can lead extensive nutritional deficiencies. The aim of this study was to investigate nutritional status, food restriction and nutrient intake status in IBD patients. A total 104 patients (food exclusion group: n = 49; food non-exclusion group: n = 55) participated in the survey. The contents were examined by 3 categories: 1) anthropometric and nutritional status; 2) diet beliefs and food restriction; and 3) nutrient intake. The malnutrition rate was significantly higher in the food exclusion group (p = 0.007) compared to food non-exclusion group. Fifty-nine percent of patients in the food exclusion group held dietary beliefs and reported modifying their intake according to their dietary belief. The most common restricted food was milk, dairy products (32.7%), raw fish (24.5%), deep-spicy foods (22.4%), and ramen (18.4%). The mean daily intake of calcium (p = 0.002), vitamin A (p < 0.001), and zinc (p = 0.001) were significantly lower in the food exclusion group. Considering malnutrition in IBD patients, nutrition education by trained dietitians is necessary for the patients to acquire disease-related knowledge and overall balanced nutrition as part of strategies in treating and preventing nutrition deficiencies.