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Inflammatory bowel disease (IBD) requires sustained patient engagement in complex therapeutic and self-management processes, making health literacy (HL) a key determinant of effective care. This cross-sectional study assessed HL levels among adults with IBD attending a public day-hospital service in Lisbon, Portugal, and examined associations with sociodemographic, lifestyle, and selected clinical variables. A convenience sample of 280 participants completed a self-administered questionnaire, including the Portuguese version of the European Health Literacy Survey Questionnaire (HLS-EU-PT-Q16). Descriptive statistics, bivariate analyses, and multiple linear regression were used. HL indices were computed and categorized into proficiency levels; domain- and competency-specific indices were also analyzed. Overall, 48.3% of participants had inadequate or problematic HL, whereas 42.5% had sufficient HL. Healthcare-related HL showed the most favourable profile, whereas health promotion emerged as the weakest domain, with domain-specific mean indices ranging from 31.8 ± 8.3 to 34.4 ± 7.4 on a 0–50 scale. Competency-specific indices indicated that appraisal and, particularly in disease prevention, application were the lowest, and item-level analyses highlighted difficulties with mental health information-seeking and evaluating or acting on media-based health information. In multivariable linear regression analysis, higher educational attainment was positively associated with HL (B = 0.89; 95% CI: 0.05 to 1.73; p = 0.039), whereas female sex was independently associated with slightly lower HL scores (B = −1.72; 95% CI: −3.33 to −0.11; p = 0.036). These findings indicate that nearly half of patients with IBD in a day-hospital setting experience HL-related vulnerabilities, especially beyond clinician-mediated care. Targeted, HL-sensitive interventions focusing on critical appraisal and decision-to-action support may enhance self-management and equity in IBD care.