The prevalence of inflammatory bowel disease (IBD) has increased worldwide. The prevalence of metabolic dysfunction associated fatty liver disease (MAFLD) has also risen. However, there is limited research on the connection between MAFLD and IBD in the Asian population. This study aims to analyze the prevalence and clinical significance of MAFLD in Taiwanese IBD patients with clinical remission. We retrospectively analyzed IBD patients who received transient elastography for liver fibrosis and controlled attenuation parameter evaluation for liver steatosis. This study enrolled 120 patients with IBD, including 45 Crohn’s disease (CD) and 75 ulcerative colitis (UC). MAFLD prevalence in IBD was 29.2%. Patients with MAFLD had a shorter disease duration (2.8 years vs. 5.3 years, p = 0.017), higher alanine aminotransferase levels (24 U/L vs. 17 U/L, p = 0.003), a lower estimated glomerular filtration rate (91.37 mL/min/1.73 m2 vs. 103.92 mL/min/1.73 m2, p = 0.004), and higher γ-glutamyl transferase (γ-GT) (24 mg/dL vs. 13 mg/dL, p < 0.001). The prevalence of significant fibrosis in IBD with MAFLD was 17.1%. Significant fibrosis was found in older age (58.5 years vs. 40 years, p = 0.004) and the high type 2 diabetes mellitus proportion (50.0% vs. 10.3%, p = 0.049). A trend of longer disease duration was found in significant fibrosis (4.9 years vs. 1.6 years, p = 0.051). The prevalence of MALFD in IBD was 29.2%. and 17.1% of them had significant fibrosis. In addition to the intestinal manifestation, the study findings remind clinicians that they should be aware of the possibility of hepatic complications for IBD patients.