Diet plays a key role in the complex etiology and treatment of inflammatory bowel disease (IBD). Most existing nutritional assessment tools neglect intake of important foods consumed or omitted specifically by IBD patients or incorporate non-Western dietary habits, making the development of appropriate dietary guidelines for (Western) IBD patients difficult. Hence, we developed a food frequency questionnaire (FFQ), the Groningen IBD Nutritional Questionnaires (GINQ-FFQ); suitable to assess dietary intake in IBD patients. To develop the GINQ-FFQ, multiple steps were taken, including: identification of IBD specific foods, a literature search, and evaluation of current dietary assessment methods. Expert views were collected and in collaboration with Wageningen University, division of Human Nutrition and Health, this semi-quantitative FFQ was developed using standard methods to obtain a valid questionnaire. Next, the GINQ-FFQ was digitized into a secure web-based environment which also embeds additional nutritional and IBD related questions. The GINQ-FFQ is an online self-administered FFQ evaluating dietary intake, taking the previous month as a reference period. It consists of 121 questions on 218 food items. This paper describes the design process of the GINQ-FFQ which assesses dietary intake especially (but not exclusively) in IBD patients. Validation of the GINQ-FFQ is needed and planned in the near future.