Introduction: The prevalences of malnutrition and sarcopenia in patients with IBD are not precisely known, and nutritional assessment is not standardized. We assessed the prevalence and risk factors of these conditions in outpatients and their impact on clinical outcomes. Methods: This prospective longitudinal study considered patients who had IBD for at least one year, were attending a tertiary IBD center, and were followed for the subsequent year. Results: In a sample of 158 consecutive patients (96 with Crohn’s disease and 62 with ulcerative colitis), the prevalence of malnutrition, according to GLIM criteria, was 13.3%. For identifying patients at risk of malnutrition, the Malnutrition Universal Screening Tool demonstrated better accuracy, (sensitivity 88.9 (65.3–98.6) and specificity 90.2 (83.8–93.4)) than the SaskIBD-NR questionnaire (sensitivity 69.3 (41.1–86.7) and specificity 60.9 (60.9–76.8)). The prevalence of sarcopenia was 34.2%. Considering clinical outcomes, sarcopenia at baseline was significantly associated with hospital admission within a year (p = 45.2% vs. 20.3%, 0.026). Conclusions: Malnutrition and sarcopenia were present in about one-third of IBD patients. Awareness should be raised among physicians caring for IBD patients about the need to evaluate patients’ nutritional statuses to help patients achieve a better quality of life.