(1) Background: Malnutrition is a highly prevalent complication in patients with inflammatory bowel diseases (IBD). It is strongly associated with poor clinical outcomes and quality of life. Screening for malnutrition risk is recommended routinely; however, current malnutrition screening tools do not incorporate IBD specific characteristics and may be less adequate for screening these patients. Therefore, we aimed to identify IBD-related risk factors for development of malnutrition. (2) Methods: A retrospective case-control study among IBD patients attending the IBD clinic of the Tel-Aviv Medical Center for ≥2 consecutive physician consultations per year during 2017–2020. Cases who had normal nutritional status and developed malnutrition between visits were compared to matched controls who maintained normal nutritional status. Detailed information was gathered from medical files, including: demographics, disease phenotype, characteristics and activity, diet altering symptoms and comorbidities, medical and surgical history, annual healthcare utility, nutritional intake and the Malnutrition Universal Screening Tool (MUST) score. Univariate and multivariate analyses were used to identify malnutrition risk factors. The independent risk factors identified were summed up to calculate the IBD malnutrition risk score (IBD-MR). (3) Results: Data of 1596 IBD patients met the initial criteria for the study. Of these, 59 patients developed malnutrition and were defined as cases (n = 59) and matched to controls (n = 59). The interval between the physician consultations was 6.2 ± 3.0 months, during which cases lost 5.3 ± 2.3 kg of body weight and controls gained 0.2 ± 2.3 kg (p < 0.001). Cases and controls did not differ in demographics, disease duration, disease phenotype or medical history. Independent IBD-related malnutrition risk factors were: 18.5 ≤ BMI ≤ 22 kg/m2 (OR = 4.71, 95%CI 1.13–19.54), high annual healthcare utility (OR = 5.67, 95%CI 1.02–31.30) and endoscopic disease activity (OR = 5.49, 95%CI 1.28–23.56). The IBD-MR was positively associated with malnutrition development independently of the MUST score (OR = 7.39, 95%CI 2.60–20.94). Among patients with low MUST scores determined during the index visit, identification of ≥2 IBD-MR factors was strongly associated with malnutrition development (OR = 8.65, 95%CI 2.21–33.82, p = 0.002). (4) Conclusions: We identified IBD-related risk factors for malnutrition, highlighting the need for a disease-specific malnutrition screening tool, which may increase malnutrition risk detection.