Malondialdehyde (MDA) is a naturally occurring organic compound produced as a byproduct of lipid peroxidation. It serves as one of the most widely recognized biomarkers for oxidative stress. Elevated levels of MDA have been observed in patients with inflammatory bowel disease (IBD), suggesting its involvement in the pathogenesis and progression of the disease. In this study, we analyzed MDA levels within a well-characterized and extensive cohort of IBD patients. Our objective was to investigate the association between MDA levels and disease characteristics in this population. This is a cross-sectional study that encompassed 197 patients with IBD. Multivariable linear regression analysis was performed to study the relationship between disease characteristics and circulating MDA. MDA was significantly associated with male sex in IBD patients but not with other demographic characteristics or classic cardiovascular risk factors. Regarding disease features such as phenotype or activity indices, their relationship with MDA was scarce. Several lipid profile molecules showed a significant association with MDA levels after multivariable analysis. Similarly, the liver fibrosis-4 index and hepatic elastography values were significantly related to higher MDA levels after adjusting for covariates. In conclusion, the sources of elevated MDA in IBD are primarily linked to lipid profile abnormalities and liver disease.