To assess nutritional intake of patients with inflammatory bowel disease (IBD), a disease-specific food frequency questionnaire (FFQ) was developed: the Groningen IBD Nutritional Questionnaire (GINQ-FFQ). Aim of this study was to assess the relative validity of the GINQ-FFQ. Between 2019 and 2022, participants of the 1000IBD cohort were included and filled out a 3-day food diary and the GINQ-FFQ. Nutritional intake of nutrients and food groups was calculated. Bland-Altman analysis was conducted for energy intake, while paired -tests and Wilcoxon signed rank tests were used for nutrient and food group intake. Additionally, group-level bias, cross-classification, and correlation analysis were performed. 142 patients (59.2% females, mean age of 49 ± 14 years) were included. Bland-Altman analysis showed a mean difference between the GINQ-FFQ and 3FD of -63.6 kcal (±638.4), with limits of agreement ranging from -1315 to 1188 kcal. Differences in energy intake was significantly associated with higher mean total energy intake ( < 0.001). When stratifying for sex, this association only was significant for males. Group-level bias showed that the GINQ-FFQ tends to result in lower intake reports for macro- and micronutrients. Ranking ability (cross-classification) of macro-, micronutrients and food groups was good. Correlation coefficients for nutrients and food groups were considered acceptable or good. Overall, the GINQ-FFQ is a valid food frequency questionnaire to assess nutritional intake specifically for patients with IBD. However, for males with high total energy intakes, dietary assessment could be less accurate.